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APR Prediction Models
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
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APR Prediction Models:
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models:
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
Structure database of aggregation related proteins and peptides
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Protein Name
Peptide Sequence
Entry ID
PDB ID
Method
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Protein/Peptide
Fibril
Aggregating complex
Inhibitor complex
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Displaying 211 to 240 records out of 565 records fetched.
Entry
PDB ID
Protein
Name
Species
Length
Mutation(s)
Class
Type
Method
Resolution (
Å
)
PMID
S-0211
3DHJ
Beta-2-microglobulin
Homo sapiens
100
W60C
Amyloid
Protein
X-RAY DIFFRACTION
2.0
18835253
S-0212
3DHM
Beta-2-microglobulin
Homo sapiens
100
D59P
Amyloid
Protein
X-RAY DIFFRACTION
1.8
18835253
S-0213
3DID
Transthyretin
Homo sapiens
127
F87M/L110M
Amyloid
Aggregating complex
X-RAY DIFFRACTION
1.383
20659897
S-0214
3DJR
Transthyretin
Homo sapiens
127
L58H
Amyloid
Protein
X-RAY DIFFRACTION
2.02
19602727
S-0215
3DJS
Transthyretin
Homo sapiens
127
L58H
Amyloid
Protein
X-RAY DIFFRACTION
1.8
19602727
S-0216
3DJT
Transthyretin
Homo sapiens
127
V30M
Amyloid
Protein
X-RAY DIFFRACTION
2.3
19602727
S-0217
3DJZ
Transthyretin
Homo sapiens
127
L55P
Amyloid
Protein
X-RAY DIFFRACTION
1.82
19602727
S-0218
3DK0
Transthyretin
Homo sapiens
127
L55P
Amyloid
Protein
X-RAY DIFFRACTION
1.87
19602727
S-0219
3DK2
Transthyretin
Homo sapiens
127
Y114H
Amyloid
Protein
X-RAY DIFFRACTION
2.35
19602727
S-0220
3DO4
Transthyretin
Homo sapiens
127
No
Amyloid
Protein
X-RAY DIFFRACTION
2.4
19602727
S-0221
3DVF
Immunoglobin kappa 1 Bence Jones protein
Homo sapiens
107
No
Amyloid
Protein
X-RAY DIFFRACTION
1.8
19361523
S-0222
3DVI
Immunoglobin kappa 1 light chain
Homo sapiens
109
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.53
19361523
S-0223
3EKC
Beta-2-microglobulin
Homo sapiens
100
W60V
Amyloid
Protein
X-RAY DIFFRACTION
1.8
19284997
S-0224
3ESN
Transthyretin
Homo sapiens
127
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.35
19191553
S-0225
3ESO
Transthyretin
Homo sapiens
127
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.31
19191553
S-0226
3ESP
Transthyretin
Homo sapiens
127
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.31
19191553
S-0227
3FC8
Transthyretin
Homo sapiens
124
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.85
19125186
S-0228
3FCB
Transthyretin
Homo sapiens
124
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.8
19125186
S-0229
3FOD
Islet Amyloid Polypeptide
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.4
19684598
S-0230
3FPO
Islet amyloid polypeptide
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.5
19684598
S-0231
3FR1
Islet amyloid polypeptide
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.85
19684598
S-0232
3FTH
Islet amyloid polypeptide
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.84
19684598
S-0233
3FTK
Islet amyloid polypeptide
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.5
19684598
S-0234
3FTL
Islet amyloid polypeptide
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.6
19684598
S-0235
3FTR
Islet amyloid polypeptide
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.61
19684598
S-0236
3FVA
Major prion protein
Cervus canadensis
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.46
19684598
S-0237
3G7V
Amylin
408
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.86
19475663
S-0238
3G7W
Amylin
393
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.75
19475663
S-0239
3GAX
Cystatin-C
Homo sapiens
120
L47C/G69C
Non-amyloid
Protein
X-RAY DIFFRACTION
1.7
20175878
S-0240
3GLZ
Transthyretin
Homo sapiens
127
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.78
19621084
Entry:S-0211
PDB ID: 3DHJ
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
H
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
C
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Beta 2 microglobulin mutant W60C; reduces aggregation capability
The stability to thermal denaturation and propensity to fibrillar aggregation have been analysed and their crystal structures were determined for Beta2-microglobulin. The experimental evidences gathered on mutant reinforce the hypothesis that conformational strain in the DE loop can affect Beta2m stability and amyloid aggregation properties.
Literature
PMID:
18835253
Author(s):
Ricagno, S., Colombo, M., de Rosa, M., Sangiovanni, E., Giorgetti, S., Raimondi, S., Bellotti, V., Bolognesi, M.
Reference:
Biochem Biophys Res Commun. 2008 Dec 5;377(1):146-50.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
100
Species:
Homo sapiens
Mutation(s):
W60C
E.C. Number:
UniProt ID:
P61769
Keyword(s):
Beta-2-microglobulin
Structure Information
PDB ID:
3DHJ
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.212
Entry:S-0212
PDB ID: 3DHM
CSV
JSON
Close ×
Structure
Press 'p' to pause
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
H
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
P
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Beta 2 microglobulin mutant W60C; Increases aggregation capability
The stability to thermal denaturation and propensity to fibrillar aggregation have been analysed and their crystal structures were determined for Beta2-microglobulin. The experimental evidences gathered on mutant reinforce the hypothesis that conformational strain in the DE loop can affect Beta2m stability and amyloid aggregation properties.
Literature
PMID:
18835253
Author(s):
Ricagno, S., Colombo, M., de Rosa, M., Sangiovanni, E., Giorgetti, S., Raimondi, S., Bellotti, V., Bolognesi, M.
Reference:
Biochem Biophys Res Commun. 2008 Dec 5;377(1):146-50.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
100
Species:
Homo sapiens
Mutation(s):
D59P
E.C. Number:
UniProt ID:
P61769
Keyword(s):
Beta-2-microglobulin
Structure Information
PDB ID:
3DHM
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.222
Entry:S-0213
PDB ID: 3DID
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
M
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
M
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
M
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
M
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 3
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
M
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
M
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 4
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
M
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
M
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6 soaked
They report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR. Stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses.
Literature
PMID:
20659897
Author(s):
Palmieri, L.de.C., Lima, L.M., Freire, J.B., Bleicher, L., Polikarpov, I., Almeida, F.C., Foguel, D.
Reference:
J Biol Chem. 2010 Oct 8;285(41):31731-41.
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Entry:
CSV
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Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
F87M/L110M
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DID
Amyloid Category:
Amyloid
Type:
Aggregating complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.383
R free:
0.20199999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACT
A
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
B
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
C
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
ZN
C
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
D
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
ZN
D
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0214
PDB ID: 3DJR
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
H
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
H
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
CRYSTAL STRUCTURE OF TRANSTHYRETIN VARIANT L58H at neutral pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
L58H
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DJR
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.02
R free:
0.228
Entry:S-0215
PDB ID: 3DJS
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
H
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
H
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin variant L58H at acidic pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
L58H
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DJS
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.217
Entry:S-0216
PDB ID: 3DJT
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
M
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
M
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin variant V30M at acidic pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
V30M
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DJT
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.3
R free:
0.253
Entry:S-0217
PDB ID: 3DJZ
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
P
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
P
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin variant L55P at neutral pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
L55P
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DJZ
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.82
R free:
0.21899999
Entry:S-0218
PDB ID: 3DK0
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
P
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
P
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin variant L55P at acidic pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
L55P
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DK0
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.87
R free:
0.222
Entry:S-0219
PDB ID: 3DK2
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
H
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
H
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin variant Y114H at acidic pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
Y114H
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DK2
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.35
R free:
0.247
Entry:S-0220
PDB ID: 3DO4
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 3
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 4
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 5
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 6
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 7
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 8
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
A
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin variant T60A at acidic pH
Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions.
Literature
PMID:
19602727
Author(s):
Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
Reference:
J Biol Chem. 2009 Sep 18;284(38):25832-41
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Structure:
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Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3DO4
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.4
R free:
0.267
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACT
A
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
ACT
B
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
ACT
G
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
ACT
H
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Entry:S-0221
PDB ID: 3DVF
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Sequence & Sec. Str.
Chain 1
1
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
25
26
S
Q
D
I
T
N
H
L
N
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
50
51
A
S
N
L
E
T
G
V
P
S
R
F
S
G
R
G
S
G
T
H
F
T
F
T
I
75
76
S
S
L
Q
P
A
D
I
A
T
Y
Y
C
Q
E
Y
D
Y
L
P
Q
T
F
G
G
100
101
G
T
K
V
E
I
K
107
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of amyloidogenic kappa 1 Bence Jones protein
Structure of amyloidogenic kappa 1 Bence Jones protein. They highlight important structural alterations in two loops flanking the dimer interface and correlate these results with the somatic mutations present in AL-12 and AL-103. These alterations are informative structural features that are likely contributing to protein instability that leads to conformational changes involved in the initial events of amyloid formation.
Literature
PMID:
19361523
Author(s):
Randles, E.G., Thompson, J.R., Martin, D.J., Ramirez-Alvarado, M.
Reference:
J Mol Biol. 2009 May 29;389(1):199-210.
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Entry:
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Structure:
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FASTA
Contact Network:
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Protein Information
Protein Name:
Immunoglobin kappa 1 Bence Jones protein
Alternative Name:
Gene Name:
Sequence Length:
107
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Amyloidogenic immunoglobulin light chain protein AL-12
Structure Information
PDB ID:
3DVF
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.266
Entry:S-0222
PDB ID: 3DVI
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Sequence & Sec. Str.
Chain 1
1
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
25
26
A
S
Q
D
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
50
51
D
A
S
N
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
75
76
I
S
S
L
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
P
Y
T
F
100
101
G
P
G
T
K
L
E
I
K
109
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of kappa 1 amyloidogenic light chain variable domain
Crystal structure of kappa 1 amyloidogenic light chain variable domain. They highlight important structural alterations in two loops flanking the dimer interface and correlate these results with the somatic mutations present in AL-12 and AL-103. These alterations are informative structural features that are likely contributing to protein instability that leads to conformational changes involved in the initial events of amyloid formation.
Literature
PMID:
19361523
Author(s):
Randles, E.G., Thompson, J.R., Martin, D.J., Ramirez-Alvarado, M.
Reference:
J Mol Biol. 2009 May 29;389(1):199-210.
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Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Immunoglobin kappa 1 light chain
Alternative Name:
Gene Name:
Sequence Length:
109
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Amyloidogenic light chain variable domain AL-103
Structure Information
PDB ID:
3DVI
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.53
R free:
0.251
Entry:S-0223
PDB ID: 3EKC
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Sequence & Sec. Str.
Chain 1
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
H
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
V
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
structure of W60V beta-2 microglobulin mutant
The W60V mutant structural features are discussed, focusing on the roles of the DE loop and of residue 60 in relation to b2m structure and its amyloid aggregation trends.
Literature
PMID:
19284997
Author(s):
Ricagno, S., Raimondi, S., Giorgetti, S., Bellotti, V., Bolognesi, M.
Reference:
Biochem Biophys Res Commun. 2009 Mar 13;380(3):543-7.
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Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
100
Species:
Homo sapiens
Mutation(s):
W60V
E.C. Number:
UniProt ID:
P61769
Keyword(s):
Beta-2-microglobulin
Structure Information
PDB ID:
3EKC
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.24100000
Entry:S-0224
PDB ID: 3ESN
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Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-2,6-dimethylbenzamide
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-2,6-dimethylbenzamide. Herein, they employ a suboptimal linker and an optimal aryl-X substructure to rank order the desirability of aryl-Z substructures--using a library of 56 N-(3,5-dibromo-4-hydroxyphenyl)benzamides. Coconsideration of amyloid inhibition potency and ex vivo plasma TTR binding selectivity data reveal that 2,6, 2,5, 2, 3,4,5, and 3,5 substituted aryls bearing small substituents generate the most potent and selective inhibitors, in descending order.
Literature
PMID:
19191553
Author(s):
Johnson, S.M., Connelly, S., Wilson, I.A., Kelly, J.W.
Reference:
J Med Chem. 2009 Feb 26;52(4):1115-25.
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Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3ESN
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
HORMONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.35
R free:
0.20199999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
DZ1
A
C15 H13 Br2 N O2
399.08
N-(3,5-dibromo-4-hydroxyphenyl)-2,6-dimethylbenzamide
Cc1cccc(c1C(=O)Nc2cc(c(c(c2)Br)O)Br)C
IFECSMFQARKPSU-UHFFFAOYSA-N
DZ1
B
C15 H13 Br2 N O2
399.08
N-(3,5-dibromo-4-hydroxyphenyl)-2,6-dimethylbenzamide
Cc1cccc(c1C(=O)Nc2cc(c(c(c2)Br)O)Br)C
IFECSMFQARKPSU-UHFFFAOYSA-N
Entry:S-0225
PDB ID: 3ESO
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Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-2,5-dichlorobenzamide
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-2,5-dichlorobenzamide. Herein, they employ a suboptimal linker and an optimal aryl-X substructure to rank order the desirability of aryl-Z substructures--using a library of 56 N-(3,5-dibromo-4-hydroxyphenyl)benzamides. Coconsideration of amyloid inhibition potency and ex vivo plasma TTR binding selectivity data reveal that 2,6, 2,5, 2, 3,4,5, and 3,5 substituted aryls bearing small substituents generate the most potent and selective inhibitors, in descending order.
Literature
PMID:
19191553
Author(s):
Johnson, S.M., Connelly, S., Wilson, I.A., Kelly, J.W.
Reference:
J Med Chem. 2009 Feb 26;52(4):1115-25.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3ESO
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
HORMONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.31
R free:
0.204
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
DZ2
A
C13 H7 Br2 Cl2 N O2
439.91
2,5-dichloro-N-(3,5-dibromo-4-hydroxyphenyl)benzamide
c1cc(c(cc1Cl)C(=O)Nc2cc(c(c(c2)Br)O)Br)Cl
IFLWCZRMFPKYBN-UHFFFAOYSA-N
DZ2
B
C13 H7 Br2 Cl2 N O2
439.91
2,5-dichloro-N-(3,5-dibromo-4-hydroxyphenyl)benzamide
c1cc(c(cc1Cl)C(=O)Nc2cc(c(c(c2)Br)O)Br)Cl
IFLWCZRMFPKYBN-UHFFFAOYSA-N
Entry:S-0226
PDB ID: 3ESP
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JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-3,5-dimethyl-4-hydroxybenzamide
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-3,5-dimethyl-4-hydroxybenzamide. Herein, they employ a suboptimal linker and an optimal aryl-X substructure to rank order the desirability of aryl-Z substructures--using a library of 56 N-(3,5-dibromo-4-hydroxyphenyl)benzamides. Coconsideration of amyloid inhibition potency and ex vivo plasma TTR binding selectivity data reveal that 2,6, 2,5, 2, 3,4,5, and 3,5 substituted aryls bearing small substituents generate the most potent and selective inhibitors, in descending order.
Literature
PMID:
19191553
Author(s):
Johnson, S.M., Connelly, S., Wilson, I.A., Kelly, J.W.
Reference:
J Med Chem. 2009 Feb 26;52(4):1115-25.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3ESP
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
HORMONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.31
R free:
0.201
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
DZ3
A
C15 H13 Br2 N O3
415.08
N-(3,5-dibromo-4-hydroxyphenyl)-4-hydroxy-3,5-dimethylbenzamide
Cc1cc(cc(c1O)C)C(=O)Nc2cc(c(c(c2)Br)O)Br
HHFKUQZPNITQLU-UHFFFAOYSA-N
DZ3
B
C15 H13 Br2 N O3
415.08
N-(3,5-dibromo-4-hydroxyphenyl)-4-hydroxy-3,5-dimethylbenzamide
Cc1cc(cc(c1O)C)C(=O)Nc2cc(c(c(c2)Br)O)Br
HHFKUQZPNITQLU-UHFFFAOYSA-N
Entry:S-0227
PDB ID: 3FC8
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
124
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
124
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin in complex with iododiflunisal-betaAlaOMe
In the present work, greatly improved inhibitors have been designed and tested by taking into account that thyroid hormones are unique in human biochemistry owing to the presence of multiple iodine atoms in their molecules which are probed to interact with specific halogen binding domains sitting at the TTR binding channel. The new TTR fibrillogenesis inhibitors are based on the diflunisal core structure because diflunisal is a registered salicylate drug with NSAID activity now undergoing clinical trials for TTR amyloid diseases.
Literature
PMID:
19125186
Author(s):
Mairal, T., Nieto, J., Pinto, M., Almeida, M.R., Gales, L., Ballesteros, A., Barluenga, J., Perez, J.J., Vazquez, J.T., Centeno, N.B., Saraiva, M.J., Damas, A.M., Planas, A., Arsequell, G., Valencia, G.
Reference:
PLoS One. 2009;4(1):e4124.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
124
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
transthyretin
Structure Information
PDB ID:
3FC8
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
HORMONE BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.85
R free:
0.21
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
IFA
A
C17 H14 F2 I N O4
461.2
METHYL N-[(2',4'-DIFLUORO-4-HYDROXY-5-IODOBIPHENYL-3-YL)CARBONYL]-BETA-ALANINATE
COC(=O)CCNC(=O)c1cc(cc(c1O)I)c2ccc(cc2F)F
ZMRRBWRMQPQQAN-UHFFFAOYSA-N
IFA
B
C17 H14 F2 I N O4
461.2
METHYL N-[(2',4'-DIFLUORO-4-HYDROXY-5-IODOBIPHENYL-3-YL)CARBONYL]-BETA-ALANINATE
COC(=O)CCNC(=O)c1cc(cc(c1O)I)c2ccc(cc2F)F
ZMRRBWRMQPQQAN-UHFFFAOYSA-N
Entry:S-0228
PDB ID: 3FCB
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
124
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
124
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of transthyretin in complex with iododiflunisal-betaAlaOH
In the present work, greatly improved inhibitors have been designed and tested by taking into account that thyroid hormones are unique in human biochemistry owing to the presence of multiple iodine atoms in their molecules which are probed to interact with specific halogen binding domains sitting at the TTR binding channel. The new TTR fibrillogenesis inhibitors are based on the diflunisal core structure because diflunisal is a registered salicylate drug with NSAID activity now undergoing clinical trials for TTR amyloid diseases.
Literature
PMID:
19125186
Author(s):
Mairal, T., Nieto, J., Pinto, M., Almeida, M.R., Gales, L., Ballesteros, A., Barluenga, J., Perez, J.J., Vazquez, J.T., Centeno, N.B., Saraiva, M.J., Damas, A.M., Planas, A., Arsequell, G., Valencia, G.
Reference:
PLoS One. 2009;4(1):e4124.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
124
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
transthyretin
Structure Information
PDB ID:
3FCB
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
HORMONE BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.226
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
IFB
A
C16 H12 F2 I N O4
447.17
N-[(2',4'-DIFLUORO-4-HYDROXY-5-IODOBIPHENYL-3-YL)CARBONYL]-BETA-ALANINE
c1cc(c(cc1F)F)c2cc(c(c(c2)I)O)C(=O)NCCC(=O)O
YZQVXOZCPWWABX-UHFFFAOYSA-N
IFB
B
C16 H12 F2 I N O4
447.17
N-[(2',4'-DIFLUORO-4-HYDROXY-5-IODOBIPHENYL-3-YL)CARBONYL]-BETA-ALANINE
c1cc(c(cc1F)F)c2cc(c(c(c2)I)O)C(=O)NCCC(=O)O
YZQVXOZCPWWABX-UHFFFAOYSA-N
Entry:S-0229
PDB ID: 3FOD
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
I
L
S
S
T
6
Chain 2
1
A
I
L
S
S
T
6
Chain 3
1
A
I
L
S
S
T
6
Chain 4
1
A
I
L
S
S
T
6
Chain 5
1
A
I
L
S
S
T
6
Chain 6
1
A
I
L
S
S
T
6
Chain 7
1
A
I
L
S
S
T
6
Chain 8
1
A
I
L
S
S
T
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
AILSST segment from Islet Amyloid Polypeptide
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
CSV
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Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Islet Amyloid Polypeptide
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
AILSST hexapeptide segment from Islet Amyloid Polypeptide
Structure Information
PDB ID:
3FOD
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.265
Entry:S-0230
PDB ID: 3FPO
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Sequence & Sec. Str.
Chain 1
1
H
S
S
N
N
F
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
HSSNNF segment from Islet Amyloid Polypeptide (IAPP or Amylin)
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
HSSNNF hexapeptide segment from Islet Amyloid Polypeptide
Structure Information
PDB ID:
3FPO
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.154
Entry:S-0231
PDB ID: 3FR1
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
N
F
L
V
H
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NFLVHS segment from Islet Amyloid Polypeptide (IAPP or Amylin)
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
Islet amyloid polypeptide
Structure Information
PDB ID:
3FR1
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.85
R free:
0.23199999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CL
A
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Entry:S-0232
PDB ID: 3FTH
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Sequence & Sec. Str.
Chain 1
1
N
F
L
V
H
S
S
7
Chain 2
1
N
F
L
V
H
S
S
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NFLVHSS segment from Islet Amyloid Polypeptide (IAPP or Amylin)
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
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Entry:
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Structure:
PDB
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FASTA
Contact Network:
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Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
NFLVHSS heptapeptide from Islet Amyloid Polypeptide
Structure Information
PDB ID:
3FTH
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.84
R free:
0.282
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0233
PDB ID: 3FTK
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Sequence & Sec. Str.
Chain 1
1
N
V
G
S
N
T
Y
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), hydrated crystal form
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
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JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
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Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
Structure Information
PDB ID:
3FTK
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 3-mer - A3
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.158
Entry:S-0234
PDB ID: 3FTL
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
N
V
G
S
N
T
Y
7
Chain 2
1
N
V
G
S
N
T
Y
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), dehydrated crystal form
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
Structure Information
PDB ID:
3FTL
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.6
R free:
0.158
Entry:S-0235
PDB ID: 3FTR
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
S
T
N
V
G
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide SSTNVG from IAPP (alternate polymorph)
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
SSTNVG FROM ISLET AMYLOID POLYPEPTIDE
Structure Information
PDB ID:
3FTR
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.61
R free:
0.253
Entry:S-0236
PDB ID: 3FVA
CSV
JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
N
N
Q
N
T
F
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NNQNTF segment from elk prion
Polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of Beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct Beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains.
Literature
PMID:
19684598
Author(s):
Wiltzius, J.J., Landau, M., Nelson, R., Sawaya, M.R., Apostol, M.I., Goldschmidt, L., Soriaga, A.B., Cascio, D., Rajashankar, K., Eisenberg, D.
Reference:
Nat Struct Mol Biol. 2009 Sep;16(9):973-8.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Cervus canadensis
Mutation(s):
No
E.C. Number:
UniProt ID:
P67986
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3FVA
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.46
R free:
0.174
Entry:S-0237
PDB ID: 3G7V
CSV
JSON
Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
A
A
L
A
A
A
Q
T
N
A
A
A
K
C
N
T
375
376
A
T
C
A
T
Q
R
L
A
N
F
L
V
H
S
S
N
N
F
G
A
I
L
S
S
400
401
T
N
V
G
S
N
T
Y
408
Chain 2
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
A
A
L
A
A
A
Q
T
N
A
A
A
K
C
N
T
375
376
A
T
C
A
T
Q
R
L
A
N
F
L
V
H
S
S
N
N
F
G
A
I
L
S
S
400
401
T
N
V
G
S
N
T
Y
408
Chain 3
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
A
A
L
A
A
A
Q
T
N
A
A
A
K
C
N
T
375
376
A
T
C
A
T
Q
R
L
A
N
F
L
V
H
S
S
N
N
F
G
A
I
L
S
S
400
401
T
N
V
G
S
N
T
Y
408
Chain 4
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
A
A
L
A
A
A
Q
T
N
A
A
A
K
C
N
T
375
376
A
T
C
A
T
Q
R
L
A
N
F
L
V
H
S
S
N
N
F
G
A
I
L
S
S
400
401
T
N
V
G
S
N
T
Y
408
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Islet Amyloid Polypeptide (IAPP or Amylin) fused to Maltose Binding Protein; The helical dimerization of IAPP accelerates fibril formation and that insulin impedes fibrillation by blocking the IAPP dimerization interface
IAPP can adopt a Alpha-helical structure at residues 8-18 and 22-27 and that molecules of IAPP dimerize. Mutational analysis suggests that this dimerization is on the pathway to fibrillation. The structure suggests how IAPP may heterodimerize with insulin. The experiments suggest the helical dimerization of IAPP accelerates fibril formation and that insulin impedes fibrillation by blocking the IAPP dimerization interface. Crystallographic studies of this helical form of IAPP are hindered by its aggressive propensity to aggregate. They have overcome this problem by chaperoning IAPP by fusion with a larger, more soluble protein. To acquire X-ray diffraction data from what is essentially an isolated IAPP molecule, they set out to protect IAPP from the inevitable fibrillation that occurs when it is unchaperoned.
Literature
PMID:
19475663
Author(s):
Wiltzius, J.J., Sievers, S.A., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2009 Jul;18(7):1521-30.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amylin
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P10997:, Amylin, Diabetes-associated peptide, Insulinoma amyloid peptide
Gene Name:
P0AEX9:, malE, b4034, JW3994, P10997:, IAPP
Sequence Length:
408
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
Structure Information
PDB ID:
3G7V
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
Sugar binding protein
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.86
R free:
0.205
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
A
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
B
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
B
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
C
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
C
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
C
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
D
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
D
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
D
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0238
PDB ID: 3G7W
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
A
A
L
A
A
A
Q
T
N
A
A
A
K
C
N
T
375
376
A
T
C
A
T
Q
R
L
A
N
F
L
V
H
S
S
N
N
393
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Islet Amyloid Polypeptide (IAPP or Amylin) fused to Maltose Binding Protein; The helical dimerization of IAPP accelerates fibril formation and that insulin impedes fibrillation by blocking the IAPP dimerization interface
IAPP can adopt a Alpha-helical structure at residues 8-18 and 22-27 and that molecules of IAPP dimerize. Mutational analysis suggests that this dimerization is on the pathway to fibrillation. The structure suggests how IAPP may heterodimerize with insulin. The experiments suggest the helical dimerization of IAPP accelerates fibril formation and that insulin impedes fibrillation by blocking the IAPP dimerization interface. Crystallographic studies of this helical form of IAPP are hindered by its aggressive propensity to aggregate. They have overcome this problem by chaperoning IAPP by fusion with a larger, more soluble protein. To acquire X-ray diffraction data from what is essentially an isolated IAPP molecule, they set out to protect IAPP from the inevitable fibrillation that occurs when it is unchaperoned.
Literature
PMID:
19475663
Author(s):
Wiltzius, J.J., Sievers, S.A., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2009 Jul;18(7):1521-30.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amylin
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P10997:, Amylin, Diabetes-associated peptide, Insulinoma amyloid peptide
Gene Name:
P0AEX9:, malE, b4034, JW3994, P10997:, IAPP
Sequence Length:
393
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
Structure Information
PDB ID:
3G7W
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
Sugar binding protein
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.75
R free:
0.19399999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MLR
A
C18 H32 O16
504.44
MALTOTRIOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O[C@@H]3[C@H](O[C@@H]([C@@H]([C@H]3O)O)O)CO)CO)O)O)O)O
FYGDTMLNYKFZSV-PXXRMHSHSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0239
PDB ID: 3GAX
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
S
P
G
K
P
P
R
L
V
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
25
26
A
L
D
F
A
V
G
E
Y
N
K
A
S
N
D
M
Y
H
S
R
A
C
Q
V
V
50
51
R
A
R
K
Q
I
V
A
G
V
N
Y
F
L
D
V
E
L
C
R
T
T
C
T
K
75
76
T
Q
P
N
L
D
N
C
P
F
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
100
101
I
Y
A
V
P
W
Q
G
T
M
T
L
S
K
S
T
C
Q
D
A
120
Chain 2
1
S
S
P
G
K
P
P
R
L
V
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
25
26
A
L
D
F
A
V
G
E
Y
N
K
A
S
N
D
M
Y
H
S
R
A
C
Q
V
V
50
51
R
A
R
K
Q
I
V
A
G
V
N
Y
F
L
D
V
E
L
C
R
T
T
C
T
K
75
76
T
Q
P
N
L
D
N
C
P
F
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
100
101
I
Y
A
V
P
W
Q
G
T
M
T
L
S
K
S
T
C
Q
D
A
120
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of monomeric human cystatin C stabilized against aggregation
They have created monomer-stabilized human cystatin C, with an engineered disulfide bond (L47C)-(G69C) between the structural elements that become separated upon domain swapping. The mutant has drastically reduced dimerization and fibril formation properties, but its inhibition of papain is unaltered.
Literature
PMID:
20175878
Author(s):
Kolodziejczyk, R., Michalska, K., Hernandez-Santoyo, A., Wahlbom, M., Grubb, A., Jaskolski, M.
Reference:
FEBS J. 2010 Apr;277(7):1726-37.
Download
Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Cystatin-C
Alternative Name:
Cystatin-3, Gamma-trace, Neuroendocrine basic polypeptide, Post-gamma-globulin
Gene Name:
CST3
Sequence Length:
120
Species:
Homo sapiens
Mutation(s):
L47C/G69C
E.C. Number:
UniProt ID:
P01034
Keyword(s):
Cystatin-C
Structure Information
PDB ID:
3GAX
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
HYDROLASE INHIBITOR
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.7
R free:
0.16699999
Entry:S-0240
PDB ID: 3GLZ
CSV
JSON
Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human Transthyretin (TTR) complexed with(E)-3-(2-(trifluoromethyl)benzylideneaminooxy)propanoic acid (inhibitor 11) 43% inhibition
TTR amyloidogenesis can be inhibited through stabilization of the native tetramer state by small molecule binding to the thyroid hormone sites of TTR. They have evaluated a new series of Beta-aminoxypropionic acids (compounds 5-21), with a single aromatic moiety (aryl or fluorenyl) linked through a flexible oxime tether to a carboxylic acid. These compounds are structurally distinct from the native ligand thyroxine and typical halogenated biaryl NSAID-like inhibitors to avoid off-target hormonal or anti-inflammatory activity.
Literature
PMID:
19621084
Author(s):
Palaninathan, S.K., Mohamedmohaideen, N.N., Orlandini, E., Ortore, G., Nencetti, S., Lapucci, A., Rossello, A., Freundlich, J.S., Sacchettini, J.C.
Reference:
PLoS One. 2009 Jul 21;4(7):e6290.
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Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3GLZ
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
HORMONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.78
R free:
0.273
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
1BD
A
C11 H10 F3 N O3
261.2
3-[({(1E)-[2-(trifluoromethyl)phenyl]methylidene}amino)oxy]propanoic acid
c1ccc(c(c1)C=NOCCC(=O)O)C(F)(F)F
NBNFAYOWJREHBN-VIZOYTHASA-N
1BD
B
C11 H10 F3 N O3
261.2
3-[({(1E)-[2-(trifluoromethyl)phenyl]methylidene}amino)oxy]propanoic acid
c1ccc(c(c1)C=NOCCC(=O)O)C(F)(F)F
NBNFAYOWJREHBN-VIZOYTHASA-N
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