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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 331 to 360 records out of 565 records fetched.
Entry
PDB ID
Protein
Name
Species
Length
Mutation(s)
Class
Type
Method
Resolution (
Å
)
PMID
S-0331
4ISV
Poly-Q
217 , 221
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.5
23777629
S-0332
4IVH
Amyloid-Beta
synthetic construct
16
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.77
S-0333
4JJ5
Poly-Q
217 , 221
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.44
23777629
S-0334
4JZ3
Proto-oncogene tyrosine-protein kinase Src
Gallus gallus
61
No
Amyloid
Protein
X-RAY DIFFRACTION
1.85
25490095
S-0335
4JZ4
Proto-oncogene tyrosine-protein kinase Src
Gallus gallus
61
No
Amyloid
Protein
X-RAY DIFFRACTION
1.56
25490095
S-0336
4K07
Immunoglobulin kappa variable 1-33
Homo sapiens
129
[del]P95
Amyloid
Protein
X-RAY DIFFRACTION
2.83
24157440
S-0337
4L3C
Beta 2-Microglobulin
276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 ,
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.64
24338476
S-0338
4M5S
alphaB crystallin
87 , 10
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.37
24711386
S-0339
4M5T
alphaB crystallin
87 , 9 , 87 , 9 , 87 , 9 , 87 , 9
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.0
24711386
S-0340
4MJH
Human Hsp27
93 , 8 , 93 , 8
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.6
24711386
S-0341
4MRB
Transthyretin
Homo sapiens
127
No
Amyloid
Protein
X-RAY DIFFRACTION
1.27
24474780
S-0342
4MRC
Transthyretin
Homo sapiens
126
S52P
Amyloid
Protein
X-RAY DIFFRACTION
1.54
24474780
S-0343
4MVI
Amyloid-Beta
188 , 40
No
Non-amyloid
Protein
X-RAY DIFFRACTION
1.7
27029347
S-0344
4MVK
Amyloid-Beta
188 , 8
No
Non-amyloid
Protein
X-RAY DIFFRACTION
1.5
27029347
S-0345
4MVL
Amyloid-Beta
188 , 40 , 40 , 40 , 40
No
Non-amyloid
Protein
X-RAY DIFFRACTION
2.3
27029347
S-0346
4NIN
Superoxide dismutase [Cu-Zn]
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.4
24344300
S-0347
4NIO
Superoxide dismutase [Cu-Zn]
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.3
24344300
S-0348
4NIP
Superoxide dismutase [Cu-Zn]
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.9
24344300
S-0349
4NP8
Islet amyloid polypeptide
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.51
19684598
S-0350
4NTP
Amyloid-Beta
synthetic construct
16
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.99
24669800
S-0351
4NTR
Amyloid-Beta
synthetic construct
16
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.7
24669800
S-0352
4NW8
Amyloid-Beta
synthetic construct
16
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
2.02
24669800
S-0353
4NW9
Amyloid-Beta
synthetic construct
16
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.66
24669800
S-0354
4OJ3
Acylphosphatase
Saccharolobus solfataricus
101
V84P
Non-amyloid
Protein
X-RAY DIFFRACTION
2.2
24893801
S-0355
4OJF
Amyloid-Beta
8 , 227 , 219
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.0
24598931
S-0356
4OJG
Acylphosphatase
Saccharolobus solfataricus
101
V84D
Non-amyloid
Protein
X-RAY DIFFRACTION
1.38
24893801
S-0357
4OJH
Acylphosphatase
Saccharolobus solfataricus
101
[del]N11/Y86E
Non-amyloid
Protein
X-RAY DIFFRACTION
1.6
24893801
S-0358
4OLR
enkephalin mutants
synthetic construct
5
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.1
24915112
S-0359
4OML
Proto-oncogene tyrosine-protein kinase Src
Gallus gallus
78
Q128R
Non-amyloid
Protein
X-RAY DIFFRACTION
1.6
25490095
S-0360
4OMN
Proto-oncogene tyrosine-protein kinase Src
Gallus gallus
77
Q128E
Non-amyloid
Protein
X-RAY DIFFRACTION
1.5
25490095
Entry:S-0331
PDB ID: 4ISV
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
Q
L
V
L
T
Q
S
S
S
A
S
F
S
L
G
A
S
A
K
L
T
C
T
L
S
25
26
R
Q
H
S
T
Y
T
I
E
W
Y
Q
Q
Q
P
L
K
P
P
K
F
V
M
E
L
50
51
K
K
D
G
S
H
S
T
G
D
G
I
P
D
R
F
S
G
S
S
S
G
A
H
R
75
76
Y
L
S
I
S
N
I
Q
P
E
D
E
A
I
Y
I
C
G
V
G
D
T
I
K
E
100
101
Q
F
V
Y
V
F
G
G
G
T
K
V
T
V
L
G
Q
P
K
S
T
P
T
L
T
125
126
V
F
P
P
S
S
E
E
L
K
E
N
K
A
T
L
V
C
L
I
S
N
F
S
P
150
151
S
G
V
T
V
A
W
K
A
N
G
T
P
I
T
Q
G
V
D
T
S
N
P
T
K
175
176
E
G
N
K
F
M
A
S
S
F
L
H
L
T
S
D
Q
W
R
S
H
N
S
F
T
200
201
C
Q
V
T
H
E
G
D
T
V
E
K
S
L
S
P
A
217
Chain 2
1
S
I
Q
L
V
Q
S
G
P
E
L
K
K
P
G
E
T
V
R
I
S
C
K
A
S
25
26
G
Y
S
F
T
T
Y
G
M
N
W
V
K
Q
A
P
G
K
G
L
K
W
M
G
W
50
51
I
N
T
Y
S
G
V
P
T
Y
A
D
D
F
K
G
R
F
A
F
S
L
E
T
S
75
76
A
S
T
A
Y
L
Q
I
N
I
L
K
N
E
D
T
A
T
Y
F
C
A
R
R
R
100
101
S
D
G
Y
S
N
Y
F
D
Y
W
G
Q
G
S
T
L
T
V
S
S
A
K
T
T
125
126
P
P
S
V
Y
P
L
A
P
G
S
A
A
Q
T
N
S
M
V
T
L
G
C
L
V
150
151
K
G
Y
F
P
E
P
V
T
V
T
W
N
S
G
S
L
S
S
G
V
H
T
F
P
175
176
A
V
L
Q
S
D
L
Y
T
L
S
S
S
V
T
V
P
S
S
T
W
P
S
Q
T
200
201
V
T
C
N
V
A
H
P
A
S
S
T
K
V
D
K
K
I
V
P
R
221
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the Fab FRAGMENT OF 1C2, A MONOCLONAL ANTIBODY SPECIFIC FOR POLY-GLUTAMINE
Three anti-polyQ antibodies-MW1, 1C2 and 3B5H10-have been extensively used to probe the conformation of polyQ. The MW1 and 1C2 antibodies have similar sequences and structures, consistent with their binding to short polyQ and their polyQ length-discrimination properties.
Literature
PMID:
23777629
Author(s):
Klein, F.A., Zeder-Lutz, G., Cousido-Siah, A., Mitschler, A., Katz, A., Eberling, P., Mandel, J.L., Podjarny, A., Trottier, Y.
Reference:
Hum Mol Genet. 2013 Oct 15;22(20):4215-23.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Poly-Q
Alternative Name:
Gene Name:
Sequence Length:
217 , 221
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4ISV
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Hetero 2-mer - AB
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.218
Entry:S-0332
PDB ID: 4IVH
CSV
JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
T
A
Q
K
L
V
F
F
A
E
D
A
X
K
X
Y
16
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of QKLVFFAED nonapeptide segment from amyloid beta incorporated into a macrocyclic beta-sheet template
Crystal structure of QKLVFFAED nonapeptide segment from amyloid beta incorporated into a macrocyclic beta-sheet template
Literature
PMID:
Author(s):
Pham, J.D., Chim, N., Goulding, C.W., Nowick, J.S.
Reference:
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:
16
Species:
synthetic construct
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
cyclo[Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-(delta-linked-Orn)-Hao-Lys-Hao-(p-bromoPhe)-Thr-(delta-linked-Orn)]
Structure Information
PDB ID:
4IVH
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
DE NOVO PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.77
R free:
0.271
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
4BF
A
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO
A
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
nan
A
Na 1
22.99
SODIUM ION
[Na+]
FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
TBU
A
C4 H10 O
74.12
TERTIARY-BUTYL ALCOHOL
CC(C)(C)O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
Entry:S-0333
PDB ID: 4JJ5
CSV
JSON
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Structure
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View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
Q
L
V
L
T
Q
S
S
S
A
S
F
S
L
G
A
S
A
K
L
T
C
T
L
S
25
26
R
Q
H
S
T
Y
T
I
E
W
Y
Q
Q
Q
P
L
K
P
P
K
F
V
M
E
L
50
51
K
K
D
G
S
H
S
T
G
D
G
I
P
D
R
F
S
G
S
S
S
G
A
H
R
75
76
Y
L
S
I
S
N
I
Q
P
E
D
E
A
I
Y
I
C
G
V
G
D
T
I
K
E
100
101
Q
F
V
Y
V
F
G
G
G
T
K
V
T
V
L
G
Q
P
K
S
T
P
T
L
T
125
126
V
F
P
P
S
S
E
E
L
K
E
N
K
A
T
L
V
C
L
I
S
N
F
S
P
150
151
S
G
V
T
V
A
W
K
A
N
G
T
P
I
T
Q
G
V
D
T
S
N
P
T
K
175
176
E
G
N
K
F
M
A
S
S
F
L
H
L
T
S
D
Q
W
R
S
H
N
S
F
T
200
201
C
Q
V
T
H
E
G
D
T
V
E
K
S
L
S
P
A
217
Chain 2
1
S
I
Q
L
V
Q
S
G
P
E
L
K
K
P
G
E
T
V
R
I
S
C
K
A
S
25
26
G
Y
S
F
T
T
Y
G
M
N
W
V
K
Q
A
P
G
K
G
L
K
W
M
G
W
50
51
I
N
T
Y
S
G
V
P
T
Y
A
D
D
F
K
G
R
F
A
F
S
L
E
T
S
75
76
A
S
T
A
Y
L
Q
I
N
I
L
K
N
E
D
T
A
T
Y
F
C
A
R
R
R
100
101
S
D
G
Y
S
N
Y
F
D
Y
W
G
Q
G
S
T
L
T
V
S
S
A
K
T
T
125
126
P
P
S
V
Y
P
L
A
P
G
S
A
A
Q
T
N
S
M
V
T
L
G
C
L
V
150
151
K
G
Y
F
P
E
P
V
T
V
T
W
N
S
G
S
L
S
S
G
V
H
T
F
P
175
176
A
V
L
Q
S
D
L
Y
T
L
S
S
S
V
T
V
P
S
S
T
W
P
S
Q
T
200
201
V
T
C
N
V
A
H
P
A
S
S
T
K
V
D
K
K
I
V
P
R
221
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
CRYSTAL STRUCTURE OF THE Fab FRAGMENT OF 1C2, A MONOCLONAL ANTIBODY SPECIFIC for POLY-GLUTAMINE
Three anti-polyQ antibodies-MW1, 1C2 and 3B5H10-have been extensively used to probe the conformation of polyQ. The MW1 and 1C2 antibodies have similar sequences and structures, consistent with their binding to short polyQ and their polyQ length-discrimination properties.
Literature
PMID:
23777629
Author(s):
Klein, F.A., Zeder-Lutz, G., Cousido-Siah, A., Mitschler, A., Katz, A., Eberling, P., Mandel, J.L., Podjarny, A., Trottier, Y.
Reference:
Hum Mol Genet. 2013 Oct 15;22(20):4215-23.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Poly-Q
Alternative Name:
Gene Name:
Sequence Length:
217 , 221
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4JJ5
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Hetero 2-mer - AB
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.44
R free:
0.28300000
Entry:S-0334
PDB ID: 4JZ3
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
S
H
M
T
F
V
A
L
Y
D
Y
E
S
R
T
E
T
D
L
S
F
K
K
G
25
26
E
R
L
Q
I
V
N
N
T
E
G
D
W
W
L
A
H
S
L
T
T
G
Q
T
G
50
51
Y
I
P
S
N
Y
V
A
P
S
D
61
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the chicken c-Src-SH3 domain intertwined dimer
They have solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6?22 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P2?2?2?, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. The residue at position 128 is connected to Glu106 at the diverging Beta-turn through a cluster of water molecules.
Literature
PMID:
25490095
Author(s):
Bacarizo, J., Martinez-Rodriguez, S., Martin-Garcia, J.M., Andujar-Sanchez, M., Ortiz-Salmeron, E., Neira, J.L., Camara-Artigas, A.
Reference:
PLoS One. 2014 Dec 9;9(12):e113224.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Proto-oncogene tyrosine-protein kinase Src
Alternative Name:
Proto-oncogene c-Src, pp60c-src
Gene Name:
SRC
Sequence Length:
61
Species:
Gallus gallus
Mutation(s):
No
E.C. Number:
2.7.10.2
UniProt ID:
P00523
Keyword(s):
Proto-oncogene tyrosine-protein kinase Src
Structure Information
PDB ID:
4JZ3
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SIGNALING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.85
R free:
0.24100000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
PEG
A
C4 H10 O3
106.12
DI(HYDROXYETHYL)ETHER
C(COCCO)O
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGE
A
C6 H14 O4
150.17
TRIETHYLENE GLYCOL
C(COCCOCCO)O
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Entry:S-0335
PDB ID: 4JZ4
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JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
S
H
M
T
F
V
A
L
Y
D
Y
E
S
R
T
E
T
D
L
S
F
K
K
G
25
26
E
R
L
Q
I
V
N
N
T
E
G
D
W
W
L
A
H
S
L
T
T
G
Q
T
G
50
51
Y
I
P
S
N
Y
V
A
P
S
D
61
Chain 2
1
G
S
H
M
T
F
V
A
L
Y
D
Y
E
S
R
T
E
T
D
L
S
F
K
K
G
25
26
E
R
L
Q
I
V
N
N
T
E
G
D
W
W
L
A
H
S
L
T
T
G
Q
T
G
50
51
Y
I
P
S
N
Y
V
A
P
S
D
61
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of chicken c-Src-SH3 domain: monomeric form
They have solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6?22 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P2?2?2?, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. The residue at position 128 is connected to Glu106 at the diverging Beta-turn through a cluster of water molecules.
Literature
PMID:
25490095
Author(s):
Bacarizo, J., Martinez-Rodriguez, S., Martin-Garcia, J.M., Andujar-Sanchez, M., Ortiz-Salmeron, E., Neira, J.L., Camara-Artigas, A.
Reference:
PLoS One. 2014 Dec 9;9(12):e113224.
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Entry:
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JSON
Structure:
PDB
CIF
FASTA
Contact Network:
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Protein Information
Protein Name:
Proto-oncogene tyrosine-protein kinase Src
Alternative Name:
Proto-oncogene c-Src, pp60c-src
Gene Name:
SRC
Sequence Length:
61
Species:
Gallus gallus
Mutation(s):
No
E.C. Number:
2.7.10.2
UniProt ID:
P00523
Keyword(s):
Proto-oncogene tyrosine-protein kinase Src
Structure Information
PDB ID:
4JZ4
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SIGNALING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.56
R free:
0.17600000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
EPE
A
C8 H18 N2 O4 S
238.3
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C1CN(CCN1CCO)CCS(=O)(=O)O
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NI
A
Ni 2
58.69
NICKEL (II) ION
[Ni+2]
VEQPNABPJHWNSG-UHFFFAOYSA-N
NI
B
Ni 2
58.69
NICKEL (II) ION
[Ni+2]
VEQPNABPJHWNSG-UHFFFAOYSA-N
Entry:S-0336
PDB ID: 4K07
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Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 2
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 3
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 4
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 5
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 6
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 7
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 8
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 9
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Chain 10
1
M
R
A
K
L
L
G
I
V
L
T
T
P
I
A
I
S
S
F
A
S
T
D
I
Q
25
26
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
S
Q
D
50
51
I
S
N
Y
L
I
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
Y
D
A
S
N
75
76
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
T
I
S
S
L
100
101
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
H
N
L
P
Y
T
F
G
P
G
T
K
125
126
L
E
I
K
129
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the amyloid-forming immunoglobulin AL-103 cis-proline 95 mutant
The deletion of proline 95a (AL-103 delP95aIns), which removes the trans-cis di-proline motif present in the patient protein AL-103, results in a dramatic increment in the thermodynamic stability and a significant delay in fibril formation kinetics with respect to AL-103. Fibril formation is pH dependent; all proteins form fibrils at pH2; reactions become slower and more stochastic as the pH increases up to pH7.
Literature
PMID:
24157440
Author(s):
Blancas-Mejia, L.M., Tischer, A., Thompson, J.R., Tai, J., Wang, L., Auton, M., Ramirez-Alvarado, M.
Reference:
J Mol Biol. 2014 Jan 23;426(2):347-61.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Immunoglobulin kappa variable 1-33
Alternative Name:
Ig kappa chain V-I region AU, Ig kappa chain V-I region Ka
Gene Name:
IGKV1-33
Sequence Length:
129
Species:
Homo sapiens
Mutation(s):
[del]P95
E.C. Number:
UniProt ID:
P01594
Keyword(s):
Amyloidogenic immunoglobulin light chain protein AL-103
Structure Information
PDB ID:
4K07
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.83
R free:
0.23600000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
SO4
B
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0337
PDB ID: 4L3C
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 2
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 3
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 4
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 5
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 6
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 7
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 8
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 9
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 10
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 11
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 12
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 13
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 14
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 15
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 16
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 17
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 18
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 19
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 20
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 21
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 22
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 23
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 24
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 25
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 26
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 27
1
G
S
H
S
M
R
Y
F
F
T
S
V
S
R
P
G
R
G
E
P
R
F
I
A
V
25
26
G
Y
V
D
D
T
Q
F
V
R
F
D
S
D
A
A
S
Q
R
M
E
P
R
A
P
50
51
W
I
E
Q
E
G
P
E
Y
W
D
G
E
T
R
K
V
K
A
H
S
Q
T
H
R
75
76
V
D
L
G
T
L
R
G
Y
Y
N
Q
S
E
A
G
S
H
T
V
Q
R
M
Y
G
100
101
C
D
V
G
S
D
W
R
F
L
R
G
Y
H
Q
Y
A
Y
D
G
K
D
Y
I
A
125
126
L
K
E
D
L
R
S
W
T
A
A
D
M
A
A
Q
T
T
K
H
K
W
E
A
A
150
151
H
V
A
E
Q
L
R
A
Y
L
E
G
T
C
V
E
W
L
R
R
Y
L
E
N
G
175
176
K
E
T
L
Q
R
T
D
A
P
K
T
H
M
T
H
H
A
V
S
D
H
E
A
T
200
201
L
R
C
W
A
L
S
F
Y
P
A
E
I
T
L
T
W
Q
R
D
G
E
D
Q
T
225
226
Q
D
T
E
L
V
E
T
R
P
A
G
D
G
T
F
Q
K
W
A
A
V
V
V
P
250
251
S
G
Q
E
Q
R
Y
T
C
H
V
Q
H
E
G
L
P
K
P
L
T
L
R
W
E
275
276
P
276
Chain 28
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
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
N
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 29
1
Y
L
L
M
W
I
T
Q
V
9
Chain 30
1
Y
L
L
M
W
I
T
Q
V
9
Chain 31
1
Y
L
L
M
W
I
T
Q
V
9
Chain 32
1
Y
L
L
M
W
I
T
Q
V
9
Chain 33
1
Y
L
L
M
W
I
T
Q
V
9
Chain 34
1
Y
L
L
M
W
I
T
Q
V
9
Chain 35
1
Y
L
L
M
W
I
T
Q
V
9
Chain 36
1
Y
L
L
M
W
I
T
Q
V
9
Chain 37
1
Y
L
L
M
W
I
T
Q
V
9
Chain 38
1
Y
L
L
M
W
I
T
Q
V
9
Chain 39
1
Y
L
L
M
W
I
T
Q
V
9
Chain 40
1
Y
L
L
M
W
I
T
Q
V
9
Chain 41
1
Y
L
L
M
W
I
T
Q
V
9
Chain 42
1
Y
L
L
M
W
I
T
Q
V
9
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of HLA-A2 in complex with D76N b2m mutant and NY-ESO1 double mutant
Human D76N Beta2-microglobulin (Beta2m) variant is the prototype of unstable and amyloidogenic protein that forms abundant extracellular fibrillar deposits. The MHCI containing D76N Beta2m (MHCI76) displays stability, dissociation patterns, and crystal structure comparable with those of the MHCI with wild type Beta2m.
Literature
PMID:
24338476
Author(s):
Halabelian, L., Ricagno, S., Giorgetti, S., Santambrogio, C., Barbiroli, A., Pellegrino, S., Achour, A., Grandori, R., Marchese, L., Raimondi, S., Mangione, P.P., Esposito, G., Al-Shawi, R., Simons, J.P., Speck, I., Stoppini, M., Bolognesi, M., Bellotti,
Reference:
J Biol Chem. 2014 Feb 7;289(6):3318-27.
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Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Beta 2-Microglobulin
Alternative Name:
MHC class I antigen A*2
Gene Name:
HLA-A, HLAA & B2M, CDABP0092, HDCMA22P & HLA-A, HLAA & B2M, CDABP0092, HDCMA22P & HLA-A, HLAA & B2M, CDABP0092, HDCMA22P & HLA-A, HLAA & B2M, CDABP0092, HDCMA22P & HLA-A, HLAA & B2M, CDABP0092, HDCMA22P & HLA-A, HLAA & B2M, CDABP0092, HDCMA22P & HLA-A, HL
Sequence Length:
276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 276 , 100 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 , 9 ,
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4L3C
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Hetero 2-mer - AB
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.64
R free:
0.218
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
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
B
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
C
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
C
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
D
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
E
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
F
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
G
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
H
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
I
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
J
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
K
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
K
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
L
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
M
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
N
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
O
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
O
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
P
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
Q
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
R
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
S
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
S
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
T
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
U
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
U
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
W
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
X
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
Y
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
Y
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Z
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CL
a
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
a
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
b
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
e
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
f
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
g
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
h
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
i
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
k
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
l
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL
p
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Entry:S-0338
PDB ID: 4M5S
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
M
R
L
E
K
D
R
F
S
V
N
L
D
V
K
H
F
S
P
E
E
L
K
V
25
26
K
V
L
G
D
V
I
E
V
H
G
K
H
E
E
R
Q
D
E
H
G
F
I
S
R
50
51
E
F
H
R
K
Y
R
I
P
A
D
V
D
P
L
T
I
T
S
S
L
S
S
D
G
75
76
V
L
T
V
N
G
P
R
K
Q
V
S
87
Chain 2
1
G
E
R
T
I
P
I
T
R
E
10
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human alphaB crystallin core domain in complex with C-terminal peptide; The structured core domain of alpha B-crystallin can prevent amyloid fibrillation and associated toxicity.
The structures of small heat-shock protein's core domains (cABC, cHSP27), each in complex with a segment of their respective C-terminal regions. Both truncated proteins dimerize, and although this interface is labile in the case of cABC, in cHSP27 the dimer can be cross-linked by an intermonomer disulfide linkage.
Literature
PMID:
24711386
Author(s):
Hochberg, G.K., Ecroyd, H., Liu, C., Cox, D., Cascio, D., Sawaya, M.R., Collier, M.P., Stroud, J., Carver, J.A., Baldwin, A.J., Robinson, C.V., Eisenberg, D.S., Benesch, J.L., Laganowsky, A.
Reference:
Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1562-70.
Download
Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
alphaB crystallin
Alternative Name:
Alpha(B)-crystallin, Heat shock protein beta-5, Renal carcinoma antigen NY-REN-27, Rosenthal fiber component
Gene Name:
CRYAB, CRYA2, HSPB5
Sequence Length:
87 , 10
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4M5S
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
CHAPERONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.37
R free:
0.187
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
SIN
A
C4 H6 O4
118.09
SUCCINIC ACID
C(CC(=O)O)C(=O)O
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Entry:S-0339
PDB ID: 4M5T
CSV
JSON
Close ×
Structure
Press 'p' to pause
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
M
R
L
E
K
D
R
F
S
V
N
L
D
V
K
H
F
S
P
E
E
L
K
V
25
26
K
V
L
G
D
V
I
E
V
H
G
K
H
E
E
R
Q
D
E
H
G
F
I
S
R
50
51
C
F
H
R
K
Y
R
I
P
A
D
V
D
P
L
T
I
T
S
S
L
S
S
D
G
75
76
V
L
T
V
N
G
P
R
K
Q
V
S
87
Chain 2
1
E
R
T
I
P
I
T
R
E
9
Chain 3
1
G
M
R
L
E
K
D
R
F
S
V
N
L
D
V
K
H
F
S
P
E
E
L
K
V
25
26
K
V
L
G
D
V
I
E
V
H
G
K
H
E
E
R
Q
D
E
H
G
F
I
S
R
50
51
C
F
H
R
K
Y
R
I
P
A
D
V
D
P
L
T
I
T
S
S
L
S
S
D
G
75
76
V
L
T
V
N
G
P
R
K
Q
V
S
87
Chain 4
1
E
R
T
I
P
I
T
R
E
9
Chain 5
1
G
M
R
L
E
K
D
R
F
S
V
N
L
D
V
K
H
F
S
P
E
E
L
K
V
25
26
K
V
L
G
D
V
I
E
V
H
G
K
H
E
E
R
Q
D
E
H
G
F
I
S
R
50
51
C
F
H
R
K
Y
R
I
P
A
D
V
D
P
L
T
I
T
S
S
L
S
S
D
G
75
76
V
L
T
V
N
G
P
R
K
Q
V
S
87
Chain 6
1
E
R
T
I
P
I
T
R
E
9
Chain 7
1
G
M
R
L
E
K
D
R
F
S
V
N
L
D
V
K
H
F
S
P
E
E
L
K
V
25
26
K
V
L
G
D
V
I
E
V
H
G
K
H
E
E
R
Q
D
E
H
G
F
I
S
R
50
51
C
F
H
R
K
Y
R
I
P
A
D
V
D
P
L
T
I
T
S
S
L
S
S
D
G
75
76
V
L
T
V
N
G
P
R
K
Q
V
S
87
Chain 8
1
E
R
T
I
P
I
T
R
E
9
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Disulfide trapped human alphaB crystallin core domain in complex with C-terminal peptide
The structures of small heat-shock protein's core domains (cABC, cHSP27), each in complex with a segment of their respective C-terminal regions. Both truncated proteins dimerize, and although this interface is labile in the case of cABC, in cHSP27 the dimer can be cross-linked by an intermonomer disulfide linkage.
Literature
PMID:
24711386
Author(s):
Hochberg, G.K., Ecroyd, H., Liu, C., Cox, D., Cascio, D., Sawaya, M.R., Collier, M.P., Stroud, J., Carver, J.A., Baldwin, A.J., Robinson, C.V., Eisenberg, D.S., Benesch, J.L., Laganowsky, A.
Reference:
Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1562-70.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
alphaB crystallin
Alternative Name:
Alpha(B)-crystallin, Heat shock protein beta-5, Renal carcinoma antigen NY-REN-27, Rosenthal fiber component
Gene Name:
CRYAB, CRYA2, HSPB5
Sequence Length:
87 , 9 , 87 , 9 , 87 , 9 , 87 , 9
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4M5T
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
CHAPERONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.244
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
SO4
C
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
SO4
D
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
SO4
E
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
SO4
F
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
SO4
G
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
SO4
H
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0340
PDB ID: 4MJH
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Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
V
S
E
I
R
H
T
A
D
R
W
R
V
S
L
D
V
N
H
F
A
P
D
E
25
26
L
T
V
K
T
K
D
G
V
V
E
I
T
G
K
H
E
E
R
Q
D
E
H
G
Y
50
51
I
S
R
C
F
T
R
K
Y
T
L
P
P
G
V
D
P
T
Q
V
S
S
S
L
S
75
76
P
E
G
T
L
T
V
E
A
P
M
P
K
L
A
T
Q
S
93
Chain 2
1
I
T
I
P
V
T
F
E
8
Chain 3
1
G
V
S
E
I
R
H
T
A
D
R
W
R
V
S
L
D
V
N
H
F
A
P
D
E
25
26
L
T
V
K
T
K
D
G
V
V
E
I
T
G
K
H
E
E
R
Q
D
E
H
G
Y
50
51
I
S
R
C
F
T
R
K
Y
T
L
P
P
G
V
D
P
T
Q
V
S
S
S
L
S
75
76
P
E
G
T
L
T
V
E
A
P
M
P
K
L
A
T
Q
S
93
Chain 4
1
I
T
I
P
V
T
F
E
8
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human Hsp27 core domain in complex with C-terminal peptide
The structures of small heat-shock protein's core domains (cABC, cHSP27), each in complex with a segment of their respective C-terminal regions. Both truncated proteins dimerize, and although this interface is labile in the case of cABC, in cHSP27 the dimer can be cross-linked by an intermonomer disulfide linkage.
Literature
PMID:
24711386
Author(s):
Hochberg, G.K., Ecroyd, H., Liu, C., Cox, D., Cascio, D., Sawaya, M.R., Collier, M.P., Stroud, J., Carver, J.A., Baldwin, A.J., Robinson, C.V., Eisenberg, D.S., Benesch, J.L., Laganowsky, A.
Reference:
Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1562-70.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Human Hsp27
Alternative Name:
28 kDa heat shock protein, Estrogen-regulated 24 kDa protein, Heat shock 27 kDa protein, Stress-responsive protein 27
Gene Name:
HSPB1, HSP27, HSP28
Sequence Length:
93 , 8 , 93 , 8
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4MJH
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
CHAPERONE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.6
R free:
0.266
Entry:S-0341
PDB ID: 4MRB
CSV
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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
Wild Type Human Transthyretin pH 7.5
Wild Type Human Transthyretin at pH 7.5. Wild-type TTR and other TTR variants has been reported to be the principal constituent of type A, cardiac amyloid fibrils formed.
Literature
PMID:
24474780
Author(s):
Mangione, P.P., Porcari, R., Gillmore, J.D., Pucci, P., Monti, M., Porcari, M., Giorgetti, S., Marchese, L., Raimondi, S., Serpell, L.C., Chen, W., Relini, A., Marcoux, J., Clatworthy, I.R., Taylor, G.W., Tennent, G.A., Robinson, C.V., Hawkins, P.N., Stop
Reference:
Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1539-44.
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Structure:
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FASTA
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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:
4MRB
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.27
R free:
0.209
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CA
A
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CA
B
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Entry:S-0342
PDB ID: 4MRC
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JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
25
26
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
50
51
P
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
75
76
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
100
101
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
K
125
126
E
126
Chain 2
1
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
25
26
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
50
51
P
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
75
76
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
100
101
P
R
R
Y
T
I
A
A
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
K
125
126
E
126
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Human Transthyretin Ser52Pro Mutant
The Ser52Pro variant of transthyretin (TTR) produces aggressive, highly penetrant, autosomal-dominant systemic amyloidosis in persons heterozygous for the causative mutation. Wild-type TTR and other TTR variants has been reported to be the principal constituent of type A, cardiac amyloid fibrils formed. In physiological conditions and under agitation the residue 49-127 proteolytic fragment rapidly and completely self-aggregates into typical amyloid fibrils. The remarkable susceptibility to such cleavage is likely caused by localized destabilization of the Beta-turn linking strands C and D caused by loss of the wild-type hydrogen-bonding network between the side chains of residues Ser52, Glu54, Ser50, and a water molecule.
Literature
PMID:
24474780
Author(s):
Mangione, P.P., Porcari, R., Gillmore, J.D., Pucci, P., Monti, M., Porcari, M., Giorgetti, S., Marchese, L., Raimondi, S., Serpell, L.C., Chen, W., Relini, A., Marcoux, J., Clatworthy, I.R., Taylor, G.W., Tennent, G.A., Robinson, C.V., Hawkins, P.N., Stop
Reference:
Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1539-44.
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Entry:
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JSON
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:
126
Species:
Homo sapiens
Mutation(s):
S52P
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
4MRC
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.54
R free:
0.228
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CA
A
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CA
B
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Entry:S-0343
PDB ID: 4MVI
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Sequence & Sec. Str.
Chain 1
1
Q
D
S
T
S
D
L
I
P
A
P
P
L
S
K
V
P
L
Q
Q
N
F
Q
D
N
25
26
Q
F
H
G
K
W
Y
V
V
G
V
A
G
N
K
S
L
R
E
D
K
D
P
W
K
50
51
M
Y
A
T
I
Y
E
L
K
E
D
K
S
Y
N
V
T
S
V
G
F
G
T
K
K
75
76
C
H
Y
K
I
R
T
F
V
P
G
S
Q
P
G
E
F
T
L
G
R
I
K
S
R
100
101
P
G
R
T
S
A
L
V
R
V
V
S
T
N
Y
N
Q
H
A
M
V
F
F
K
V
125
126
V
Q
Q
N
R
E
S
F
N
I
T
L
Y
G
R
T
K
E
L
T
S
E
L
K
E
150
151
N
F
I
R
F
S
K
S
L
G
L
P
E
N
H
I
V
F
P
V
P
I
D
Q
C
175
176
I
D
G
S
A
W
S
H
P
Q
F
E
K
188
Chain 2
1
D
A
E
F
R
H
D
S
G
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
G
A
I
I
G
L
M
V
G
G
V
V
40
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide Abeta(1-40)
Amyloid beta (ABeta) peptides, in particular ABeta42 and ABeta40, exert neurotoxic effects and their overproduction leads to amyloid deposits in the brain, thus constituting an important biomolecular target for treatments of Alzheimer's disease (AD). They describe the engineering of cognate Anticalins as a novel type of neutralizing protein reagent based on the human lipocalin scaffold.
Literature
PMID:
27029347
Author(s):
Rauth, S., Hinz, D., Borger, M., Uhrig, M., Mayhaus, M., Riemenschneider, M., Skerra, A.
Reference:
Biochem J. 2016 Jun 1;473(11):1563-78.
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Entry:
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Structure:
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CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
25 kDa alpha-2-microglobulin-related subunit of MMP-9, Lipocalin-2, Oncogene 24p3, Siderocalin, p25 & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Prote
Gene Name:
LCN2, HNL, NGAL & APP, A4, AD1
Sequence Length:
188 , 40
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4MVI
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
PROTEIN BINDING/PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.7
R free:
0.212
Entry:S-0344
PDB ID: 4MVK
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Sequence & Sec. Str.
Chain 1
1
Q
D
S
T
S
D
L
I
P
A
P
P
L
S
K
V
P
L
Q
Q
N
F
Q
D
N
25
26
Q
F
H
G
K
W
Y
V
V
G
V
A
G
N
K
S
L
R
E
D
K
D
P
W
K
50
51
M
Y
A
T
I
Y
E
L
K
E
D
K
S
Y
N
V
T
S
V
G
F
G
T
K
K
75
76
C
H
Y
K
I
R
T
F
V
P
G
S
Q
P
G
E
F
T
L
G
R
I
K
S
R
100
101
P
G
R
T
S
A
L
V
R
V
V
S
T
N
Y
N
Q
H
A
M
V
F
F
K
V
125
126
V
Q
Q
N
R
E
S
F
N
I
T
L
Y
G
R
T
K
E
L
T
S
E
L
K
E
150
151
N
F
I
R
F
S
K
S
L
G
L
P
E
N
H
I
V
F
P
V
P
I
D
Q
C
175
176
I
D
G
S
A
W
S
H
P
Q
F
E
K
188
Chain 2
1
X
V
F
F
A
E
D
X
8
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide fragment VFFAED
Amyloid beta (ABeta) peptides, in particular ABeta42 and ABeta40, exert neurotoxic effects and their overproduction leads to amyloid deposits in the brain, thus constituting an important biomolecular target for treatments of Alzheimer's disease (AD). They describe the engineering of cognate Anticalins as a novel type of neutralizing protein reagent based on the human lipocalin scaffold.
Literature
PMID:
27029347
Author(s):
Rauth, S., Hinz, D., Borger, M., Uhrig, M., Mayhaus, M., Riemenschneider, M., Skerra, A.
Reference:
Biochem J. 2016 Jun 1;473(11):1563-78.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
25 kDa alpha-2-microglobulin-related subunit of MMP-9, Lipocalin-2, Oncogene 24p3, Siderocalin, p25 & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Prote
Gene Name:
LCN2, HNL, NGAL & APP, A4, AD1
Sequence Length:
188 , 8
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4MVK
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
PROTEIN BINDING/PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.18600000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACE
B
C2 H4 O
44.05
ACETYL GROUP
CC=O
IKHGUXGNUITLKF-UHFFFAOYSA-N
NH2
B
H2 N
16.02
AMINO GROUP
[NH2]
QGZKDVFQNNGYKY-UHFFFAOYAF
Entry:S-0345
PDB ID: 4MVL
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Sequence & Sec. Str.
Chain 1
1
Q
D
S
T
S
D
L
I
P
A
P
P
L
S
K
V
P
L
Q
Q
N
F
Q
D
N
25
26
Q
F
H
G
K
W
Y
V
V
G
A
A
G
N
V
L
L
R
E
D
K
D
P
L
K
50
51
M
Y
A
T
I
Y
E
L
K
E
D
K
S
Y
N
V
T
S
V
G
F
D
D
K
K
75
76
C
L
Y
K
I
R
T
F
V
P
G
S
Q
P
G
E
F
T
L
G
R
I
K
S
E
100
101
P
G
G
T
S
W
L
V
R
V
V
S
T
N
Y
N
Q
H
A
M
V
F
F
K
E
125
126
V
A
Q
N
R
E
T
F
N
I
T
L
Y
G
R
T
K
E
L
T
S
E
L
K
E
150
151
N
F
I
R
F
S
K
S
L
G
L
P
E
N
H
I
V
F
P
V
P
I
D
Q
C
175
176
I
D
G
S
A
W
S
H
P
Q
F
E
K
188
Chain 2
1
Q
D
S
T
S
D
L
I
P
A
P
P
L
S
K
V
P
L
Q
Q
N
F
Q
D
N
25
26
Q
F
H
G
K
W
Y
V
V
G
A
A
G
N
V
L
L
R
E
D
K
D
P
L
K
50
51
M
Y
A
T
I
Y
E
L
K
E
D
K
S
Y
N
V
T
S
V
G
F
D
D
K
K
75
76
C
L
Y
K
I
R
T
F
V
P
G
S
Q
P
G
E
F
T
L
G
R
I
K
S
E
100
101
P
G
G
T
S
W
L
V
R
V
V
S
T
N
Y
N
Q
H
A
M
V
F
F
K
E
125
126
V
A
Q
N
R
E
T
F
N
I
T
L
Y
G
R
T
K
E
L
T
S
E
L
K
E
150
151
N
F
I
R
F
S
K
S
L
G
L
P
E
N
H
I
V
F
P
V
P
I
D
Q
C
175
176
I
D
G
S
A
W
S
H
P
Q
F
E
K
188
Chain 3
1
Q
D
S
T
S
D
L
I
P
A
P
P
L
S
K
V
P
L
Q
Q
N
F
Q
D
N
25
26
Q
F
H
G
K
W
Y
V
V
G
A
A
G
N
V
L
L
R
E
D
K
D
P
L
K
50
51
M
Y
A
T
I
Y
E
L
K
E
D
K
S
Y
N
V
T
S
V
G
F
D
D
K
K
75
76
C
L
Y
K
I
R
T
F
V
P
G
S
Q
P
G
E
F
T
L
G
R
I
K
S
E
100
101
P
G
G
T
S
W
L
V
R
V
V
S
T
N
Y
N
Q
H
A
M
V
F
F
K
E
125
126
V
A
Q
N
R
E
T
F
N
I
T
L
Y
G
R
T
K
E
L
T
S
E
L
K
E
150
151
N
F
I
R
F
S
K
S
L
G
L
P
E
N
H
I
V
F
P
V
P
I
D
Q
C
175
176
I
D
G
S
A
W
S
H
P
Q
F
E
K
188
Chain 4
1
Q
D
S
T
S
D
L
I
P
A
P
P
L
S
K
V
P
L
Q
Q
N
F
Q
D
N
25
26
Q
F
H
G
K
W
Y
V
V
G
A
A
G
N
V
L
L
R
E
D
K
D
P
L
K
50
51
M
Y
A
T
I
Y
E
L
K
E
D
K
S
Y
N
V
T
S
V
G
F
D
D
K
K
75
76
C
L
Y
K
I
R
T
F
V
P
G
S
Q
P
G
E
F
T
L
G
R
I
K
S
E
100
101
P
G
G
T
S
W
L
V
R
V
V
S
T
N
Y
N
Q
H
A
M
V
F
F
K
E
125
126
V
A
Q
N
R
E
T
F
N
I
T
L
Y
G
R
T
K
E
L
T
S
E
L
K
E
150
151
N
F
I
R
F
S
K
S
L
G
L
P
E
N
H
I
V
F
P
V
P
I
D
Q
C
175
176
I
D
G
S
A
W
S
H
P
Q
F
E
K
188
Chain 5
1
D
A
E
F
R
H
D
S
G
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
G
A
I
I
G
L
M
V
G
G
V
V
40
Chain 6
1
D
A
E
F
R
H
D
S
G
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
G
A
I
I
G
L
M
V
G
G
V
V
40
Chain 7
1
D
A
E
F
R
H
D
S
G
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
G
A
I
I
G
L
M
V
G
G
V
V
40
Chain 8
1
D
A
E
F
R
H
D
S
G
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
G
A
I
I
G
L
M
V
G
G
V
V
40
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of an engineered lipocalin (Anticalin H1GA) in complex with the Alzheimer amyloid peptide Abeta1-40
Amyloid beta (ABeta) peptides, in particular ABeta42 and ABeta40, exert neurotoxic effects and their overproduction leads to amyloid deposits in the brain, thus constituting an important biomolecular target for treatments of Alzheimer's disease (AD). They describe the engineering of cognate Anticalins as a novel type of neutralizing protein reagent based on the human lipocalin scaffold.
Literature
PMID:
27029347
Author(s):
Rauth, S., Hinz, D., Borger, M., Uhrig, M., Mayhaus, M., Riemenschneider, M., Skerra, A.
Reference:
Biochem J. 2016 Jun 1;473(11):1563-78.
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Structure:
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Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
25 kDa alpha-2-microglobulin-related subunit of MMP-9, Lipocalin-2, Oncogene 24p3, Siderocalin, p25 & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Prote
Gene Name:
LCN2, HNL, NGAL & APP, A4, AD1 & APP, A4, AD1 & APP, A4, AD1 & APP, A4, AD1
Sequence Length:
188 , 40 , 40 , 40 , 40
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
4MVL
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
PROTEIN BINDING/PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.3
R free:
0.27899999
Entry:S-0346
PDB ID: 4NIN
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Sequence & Sec. Str.
Chain 1
1
D
S
V
I
S
L
S
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
DSVISLS segment 101-107 from Human Superoxide Dismutase
The atomic structures of two fibril-forming segments from the C terminus, (101)DSVISLS(107) and (147)GVIGIAQ(153), reveal tightly packed Beta-sheets with steric zipper interfaces characteristic of the amyloid state. Based on these structures, we conclude that both C-terminal segments are likely to form aggregates if available for interaction. Proline substitutions in (101)DSVISLS(107) and (147)GVIGIAQ(153) impaired nucleation and fibril growth of full-length protein, confirming that these segments participate in aggregate formation.
Literature
PMID:
24344300
Author(s):
Ivanova, M.I., Sievers, S.A., Guenther, E.L., Johnson, L.M., Winkler, D.D., Galaleldeen, A., Sawaya, M.R., Hart, P.J., Eisenberg, D.S.
Reference:
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):197-201.
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Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P00441
Keyword(s):
DSVISLS segment from Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
4NIN
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.228
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0347
PDB ID: 4NIO
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Sequence & Sec. Str.
Chain 1
1
G
V
T
G
I
A
Q
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GVTGIAQ segment 147-153 from Human Superoxide Dismutase with I149T mutation associated with a familial form of amyotrophic lateral sclerosis
The atomic structures of two fibril-forming segments from the C terminus, (101)DSVISLS(107) and (147)GVIGIAQ(153), reveal tightly packed Beta-sheets with steric zipper interfaces characteristic of the amyloid state. Based on these structures, we conclude that both C-terminal segments are likely to form aggregates if available for interaction. Proline substitutions in (101)DSVISLS(107) and (147)GVIGIAQ(153) impaired nucleation and fibril growth of full-length protein, confirming that these segments participate in aggregate formation.
Literature
PMID:
24344300
Author(s):
Ivanova, M.I., Sievers, S.A., Guenther, E.L., Johnson, L.M., Winkler, D.D., Galaleldeen, A., Sawaya, M.R., Hart, P.J., Eisenberg, D.S.
Reference:
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):197-201.
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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:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P00441
Keyword(s):
GVTGIAQ segment from Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
4NIO
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.3
R free:
0.233
Entry:S-0348
PDB ID: 4NIP
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Sequence & Sec. Str.
Chain 1
1
G
V
I
G
I
A
Q
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GVIGIAQ segment 147-153 from Human Superoxide Dismutase
The atomic structures of two fibril-forming segments from the C terminus, (101)DSVISLS(107) and (147)GVIGIAQ(153), reveal tightly packed Beta-sheets with steric zipper interfaces characteristic of the amyloid state. Based on these structures, we conclude that both C-terminal segments are likely to form aggregates if available for interaction. Proline substitutions in (101)DSVISLS(107) and (147)GVIGIAQ(153) impaired nucleation and fibril growth of full-length protein, confirming that these segments participate in aggregate formation.
Literature
PMID:
24344300
Author(s):
Ivanova, M.I., Sievers, S.A., Guenther, E.L., Johnson, L.M., Winkler, D.D., Galaleldeen, A., Sawaya, M.R., Hart, P.J., Eisenberg, D.S.
Reference:
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):197-201.
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Entry:
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Structure:
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FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P00441
Keyword(s):
GVTGIAQ segment from Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
4NIP
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.9
R free:
0.249
Entry:S-0349
PDB ID: 4NP8
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Sequence & Sec. Str.
Chain 1
1
V
Q
I
V
Y
K
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide VQIVYK from the second repeat region of tau (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.
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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):
Structure of an amyloid forming peptide VQIVYK
Structure Information
PDB ID:
4NP8
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.51
R free:
0.196
Entry:S-0350
PDB ID: 4NTP
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 2
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 3
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 4
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 5
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 6
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 7
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 8
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 9
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 10
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 11
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 12
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 13
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 14
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 15
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 16
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
X-ray crystallographic structures of trimers and higher-order oligomeric assemblies of a peptide derived from A beta (17-36)
A peptide derived from ABeta17-36 crystallizes to form trimers that further associate to form higher-order oligomers. The trimers consist of three highly twisted Beta-hairpins in a triangular arrangement. Two trimers associate face-to-face in the crystal lattice to form a hexamer; four trimers in a tetrahedral arrangement about a central cavity form a dodecamer. These structures provide a working model for the structures of oligomers associated with neurodegeneration in Alzheimer's disease.
Literature
PMID:
24669800
Author(s):
Spencer, R.K., Li, H., Nowick, J.S.
Reference:
J Am Chem Soc. 2014 Apr 16;136(15):5595-8.
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Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:
16
Species:
synthetic construct
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
Structure Information
PDB ID:
4NTP
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 16-mer - A16
PDB Classification:
de novo protein
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.99
R free:
0.24600000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
nan
A
Na 1
22.99
SODIUM ION
[Na+]
FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
A
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
A
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
CL
B
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
ORN
B
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
B
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
B
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
C
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
C
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
C
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
D
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
D
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
D
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
CL
E
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
nan
E
Na 1
22.99
SODIUM ION
[Na+]
FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN
E
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
E
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
E
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
F
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
F
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
F
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
CL
G
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
ORN
G
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
G
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
G
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
CL
H
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
ORN
H
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
H
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
H
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
I
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
I
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
I
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
J
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
J
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
J
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
K
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
K
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
K
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
L
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
L
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
L
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
M
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
M
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
M
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
N
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
N
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
N
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN
O
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
O
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
O
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
CL
P
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
ORN
P
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI
P
C9 H10 I N O2
291.09
IODO-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)I
PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR
P
C3 H7 N O2
89.09
SARCOSINE
CNCC(=O)O
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
Entry:S-0351
PDB ID: 4NTR
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 2
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
Chain 3
1
A
L
V
F
F
A
E
D
A
A
I
I
G
L
A
V
16
