CPAD 2.0

Entry	PDB ID	Protein Name	Species	Length	Mutation(s)	Class	Type	Method	Resolution (Å)	PMID
S-0301	3SGR	Alpha-crystallin B chain	Homo sapiens	25	K11V-TR	Amyloid	Fibril	X-RAY DIFFRACTION	2.17	22403391
S-0302	3SGS	Alpha-crystallin B chain	Homo sapiens	6	G6V	Amyloid	Fibril	X-RAY DIFFRACTION	1.7	22403391
S-0303	3SSG	Transthyretin	Homo sapiens	127	L55P	Amyloid	Aggregating complex	X-RAY DIFFRACTION	2.0	22120741
S-0304	3T4G	Amyloid-Beta		14	No	Non-amyloid	Fibril	X-RAY DIFFRACTION	1.7	23089868
S-0305	3TCT	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.3	22645360
S-0306	3U79	AL-103	Homo sapiens	111	Y32F/Y96F	Amyloid	Protein	X-RAY DIFFRACTION	1.62
S-0307	3U7A	AL-09	Homo sapiens	110	Y32F/Y96F	Amyloid	Protein	X-RAY DIFFRACTION	2.0
S-0308	3ZPK	Transthyretin	Rattus norvegicus	11	No	Amyloid	Fibril	ELECTRON MICROSCOPY, SOLID-STATE NMR		23513222
S-0309	4BXL	Alpha-synuclein		46 , 22	No	Non-amyloid	Inhibitor complex	SOLUTION NMR		24623599
S-0310	4D9Z	Lysozyme C	Gallus gallus	129	No	Amyloid	Protein	X-RAY DIFFRACTION	1.71	26926993
S-0311	4DC4	Lysozyme C	Gallus gallus	129	No	Amyloid	Protein	X-RAY DIFFRACTION	2.65	26926993
S-0312	4E0K	Beta-2-microglobulin	Homo sapiens	6	No	Amyloid	Fibril	X-RAY DIFFRACTION	0.97	23213214
S-0313	4E0L	Beta-2-microglobulin	Homo sapiens	14	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.7	23213214
S-0314	4E0M	Microtubule-associated protein tau	Homo sapiens	14	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.75	23213214
S-0315	4E0N	Microtubule-associated protein tau	Homo sapiens	14	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.65	23213214
S-0316	4E0O	Microtubule-associated protein tau	Homo sapiens	14	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.82	23213214
S-0317	4E1H	Prion protein		6	No	Non-amyloid	Fibril	X-RAY DIFFRACTION	1.4	23808589
S-0318	4E1I	Prion protein		6	No	Non-amyloid	Fibril	X-RAY DIFFRACTION	2.03	23808589
S-0319	4EOF	Lysozyme C	Gallus gallus	129	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.83	26926993
S-0320	4F37	Amyloid-Beta		124 , 228 , 228 , 219 , 219	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.57	23609990
S-0321	4HIQ	Transthyretin	Homo sapiens	127	V122I	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.18	23716704
S-0322	4HIS	Transthyretin	Homo sapiens	127	V122I	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.2	23716704
S-0323	4HIX	Amyloid-Beta		28 , 227 , 220	No	Amyloid	Fibril complex	X-RAY DIFFRACTION	2.2	23416764
S-0324	4I0C	Lysozyme		130 , 132 , 132	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.95	23919586
S-0325	4I85	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.67	23792159
S-0326	4I87	Transthyretin	Homo sapiens	127	I84S	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.69	23792159
S-0327	4I89	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.69	23792159
S-0328	4II8	Lysozyme C	Gallus gallus	129	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.88	26926993
S-0329	4IP8	Serum amyloid A-1 protein	Homo sapiens	105	No	Amyloid	Protein	X-RAY DIFFRACTION	2.19	24706838
S-0330	4IP9	Serum amyloid A-1 protein	Homo sapiens	111	No	Amyloid	Protein	X-RAY DIFFRACTION	2.5	24706838

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

K

L

K

V

L

G

D

V

I

E

V

G

K

L

K

V

L

G

D

V

I

E

V

25

Chain 2

1

G

K

L

K

V

L

G

D

V

I

E

V

G

K

L

K

V

L

G

D

V

I

E

V

25

Chain 3

1

G

K

L

K

V

L

G

D

V

I

E

V

G

K

L

K

V

L

G

D

V

I

E

V

25

Chain 4

1

G

K

L

K

V

L

G

D

V

I

E

V

G

K

L

K

V

L

G

D

V

I

E

V

25

Chain 5

1

G

K

L

K

V

L

G

D

V

I

E

V

G

K

L

K

V

L

G

D

V

I

E

V

25

Chain 6

1

G

K

L

K

V

L

G

D

V

I

E

V

G

K

L

K

V

L

G

D

V

I

E

V

25

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L

They identify a segment of the amyloid-forming protein AlphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: Beta-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that was termed cylindrin.

Literature

PMID:	22403391
Author(s):	Laganowsky, A., Liu, C., Sawaya, M.R., Whitelegge, J.P., Park, J., Zhao, M., Pensalfini, A., Soriaga, A.B., Landau, M., Teng, P.K., Cascio, D., Glabe, C., Eisenberg, D.
Reference:	Science. 2012 Mar 9;335(6073):1228-31.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Alpha-crystallin B chain
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:	25
Species:	Homo sapiens
Mutation(s):	K11V-TR
E.C. Number:
UniProt ID:	P02511
Keyword(s):	Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L

Structure Information

PDB ID:	3SGR
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.17
R free:	0.23399999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MPD	E	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N

Structure

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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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

P

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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

Structure of transthyretin L55P in complex with Zn

The effect of Zn(2+) in increasing TTR L55P amyloidogenecity has been reported. Crystals of the TTR L55P-Zn(2+) complex were grown under conditions similar to those leading to higher amyloidogenic potential of the variant protein and the three-dimensional structure of the complex was determined by X-ray crystallography. Two different tetrahedral Zn(2+)-binding sites were identified: one cross-links two tetramers, while the other lies at the interface between two monomers in a dimer. The association of monomers involving the two Zn(2+)-binding sites leads to a bidimensional array with a cross-Beta structure.

Literature

PMID:	22120741
Author(s):	Castro-Rodrigues, A.F., Gales, L., Saraiva, M.J., Damas, A.M.
Reference:	Acta Crystallogr D Biol Crystallogr. 2011 Dec;67(Pt 12):1035-44.

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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:	3SSG
Amyloid Category:	Amyloid
Type:	Aggregating complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.0
R free:	0.247

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CAC	A	C2 H6 As O2 -1	136.99	CACODYLATE ION	C[As](=O)(C)[O-]	OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN	A	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

I

G

L

M

V

A

K

F

X

Y

K

14

Chain 2

1

A

I

G

L

M

V

A

K

F

X

Y

K

14

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

AIIGLMV segment from Alzheimer's Amyloid-Beta displayed on 54-membered macrocycle scaffold; Amyloid beta-sheet mimics (ABSMs) to antagonize the aggregation of various amyloid proteins, thereby reducing the toxicity of amyloid aggregates

They introduce a family of robust Beta-sheet macrocycles that can serve as a platform to display a variety of heptapeptide sequences from different amyloid proteins. They have tailored these amyloid Beta-sheet mimics (ABSMs) to antagonize the aggregation of various amyloid proteins, thereby reducing the toxicity of amyloid aggregates. We describe the structures and inhibitory properties of ABSMs containing amyloidogenic peptides from the amyloid-Beta peptide

Literature

PMID:	23089868
Author(s):	Cheng, P.N., Liu, C., Zhao, M., Eisenberg, D., Nowick, J.S.
Reference:	Nat Chem. 2012 Nov;4(11):927-33.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:	14
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K

Structure Information

PDB ID:	3T4G
Amyloid Category:	Non-amyloid
Type:	Fibril
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	UNKNOWN FUNCTION
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.7
R free:	0.27399999

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
MPD	A	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF	B	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	B	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
MPD	B	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N

Structure

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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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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

Structure of wild-type TTR in complex with tafamidis

Tetramer dissociation is the rate-limiting step in TTR amyloidogenesis, targeted therapies have focused on small molecules that kinetically stabilize the tetramer, inhibiting TTR amyloid fibril formation. tafamidis meglumine (Fx-1006A), has recently completed Phase II/III trials for the treatment of Transthyretin Type Familial Amyloid Polyneuropathy (TTR-FAP) and demonstrated a slowing of disease progression in patients heterozygous for the V30M TTR mutation. Tafamidis binds selectively and with negative cooperativity to the two normally unoccupied thyroxine-binding sites of the tetramer, and kinetically stabilizes TTR. Patient-derived amyloidogenic variants of TTR, including kinetically and thermodynamically less stable mutants, are also stabilized by tafamidis binding.

Literature

PMID:	22645360
Author(s):	Bulawa, C.E., Connelly, S., Devit, M., Wang, L., Weigel, C., Fleming, J.A., Packman, J., Powers, E.T., Wiseman, R.L., Foss, T.R., Wilson, I.A., Kelly, J.W., Labaudiniere, R.
Reference:	Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9629-34.

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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:	3TCT
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.3
R free:	0.192

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
3MI	A	C14 H7 Cl2 N O3	308.12	2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid	c1cc2c(cc1C(=O)O)oc(n2)c3cc(cc(c3)Cl)Cl	TXEIIPDJKFWEEC-UHFFFAOYSA-N
3MI	B	C14 H7 Cl2 N O3	308.12	2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid	c1cc2c(cc1C(=O)O)oc(n2)c3cc(cc(c3)Cl)Cl	TXEIIPDJKFWEEC-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 2

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 3

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 4

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 5

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 6

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 7

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Chain 8

1

S

T

D

I

Q

M

T

Q

S

P

S

L

S

A

S

V

G

D

R

V

T

I

T

C

25

26

Q

A

S

Q

D

I

S

N

F

L

I

W

Y

Q

K

P

G

K

A

P

K

L

I

50

51

Y

D

A

S

N

L

E

T

G

V

P

S

R

F

S

G

S

G

S

G

T

D

F

T

F

75

76

T

I

S

L

Q

P

E

D

I

A

T

Y

C

Q

Y

H

N

L

P

F

T

100

101

F

G

P

G

T

K

L

E

I

K

R

111

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Tyrosine Residues mediate crucial interactions in amyloid formation for immunoglobulin light chains

Literature

PMID:
Author(s):	DiCostanzo, A.C., Thompson, J.R., Peterson, F.C., F Volkman, B., Ramirez-Alvarado, M.
Reference:

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	AL-103
Alternative Name:	Immunoglobin
Gene Name:
Sequence Length:	111
Species:	Homo sapiens
Mutation(s):	Y32F/Y96F
E.C. Number:
UniProt ID:
Keyword(s):	Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain

Structure Information

PDB ID:	3U79
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.62
R free:	0.223

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
ZN	A	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	B	C2 H3 O2 -1	59.04	ACETATE ION	CC(=O)[O-]	QTBSBXVTEAMEQO-UHFFFAOYSA-M
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
ACT	E	C2 H3 O2 -1	59.04	ACETATE ION	CC(=O)[O-]	QTBSBXVTEAMEQO-UHFFFAOYSA-M
MES	E	C6 H13 N O4 S	195.24	2-(N-MORPHOLINO)-ETHANESULFONIC ACID	C1COCC[NH+]1CCS(=O)(=O)[O-]	SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	E	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	F	C2 H3 O2 -1	59.04	ACETATE ION	CC(=O)[O-]	QTBSBXVTEAMEQO-UHFFFAOYSA-M
ZN	F	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	G	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	H	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Lysozyme at 318K; At 45C, in wells containing 1.2-1.3 M NaCl in mother liquid, only 1-2 spherulites were formed along with normal tetragonal and orthorhombic crystals

They report results on how heat transforms globular protein, lysozyme into building block of Beta-amyloids. Light scattering experiments showed formation of lower order associated species around 50-70?Â°C followed by rapid cooperativity to Beta-amyloid fibrils. crystallization drops set at higher temperatures either led to aggregates or spherulites. The latter possess an amorphous Beta-fibril rich core with thin crystalline needles projecting outwards. Diffraction of the crystalline outgrowths revealed novel dimers and trimers of lysozyme where individual chains were similar to monomer with marginal gain in Beta-sheet content. Overall this work concludes that heat induced weakly associated structures of lysozyme are the first step towards its amyloid formation.

Literature

PMID:	26926993
Author(s):	Sharma, P., Verma, N., Singh, P.K., Korpole, S., Ashish
Reference:	Sci Rep. 2016 Mar 1;6:22475.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Lysozyme C
Alternative Name:	1, 4-beta-N-acetylmuramidase C, Allergen Gal d IV
Gene Name:	LYZ
Sequence Length:	129
Species:	Gallus gallus
Mutation(s):	No
E.C. Number:	3.2.1.17
UniProt ID:	P00698
Keyword(s):	Lysozyme C

Structure Information

PDB ID:	4D9Z
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.71
R free:	0.228

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
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Chain 2

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Chain 3

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Lysozyme Trimer

They report results on how heat transforms globular protein, lysozyme into building block of Beta-amyloids. Light scattering experiments showed formation of lower order associated species around 50-70?Â°C followed by rapid cooperativity to Beta-amyloid fibrils. crystallization drops set at higher temperatures either led to aggregates or spherulites. The latter possess an amorphous Beta-fibril rich core with thin crystalline needles projecting outwards. Diffraction of the crystalline outgrowths revealed novel dimers and trimers of lysozyme where individual chains were similar to monomer with marginal gain in Beta-sheet content. Overall this work concludes that heat induced weakly associated structures of lysozyme are the first step towards its amyloid formation.

Literature

PMID:	26926993
Author(s):	Sharma, P., Verma, N., Singh, P.K., Korpole, S., Ashish
Reference:	Sci Rep. 2016 Mar 1;6:22475.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Lysozyme C
Alternative Name:	1, 4-beta-N-acetylmuramidase C, Allergen Gal d IV
Gene Name:	LYZ
Sequence Length:	129
Species:	Gallus gallus
Mutation(s):	No
E.C. Number:	3.2.1.17
UniProt ID:	P00698
Keyword(s):	Lysozyme C

Structure Information

PDB ID:	4DC4
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.65
R free:	0.3

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
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	B	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	B	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
nan	B	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

D

W

S

F

Y

6

Chain 2

1

K

D

W

S

F

Y

6

Chain 3

1

K

D

W

S

F

Y

6

Chain 4

1

K

D

W

S

F

Y

6

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2 Microglobulin (58-63)

They designed out-of-register Beta-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register Beta-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.

Literature

PMID:	23213214
Author(s):	Liu, C., Zhao, M., Jiang, L., Cheng, P.N., Park, J., Sawaya, M.R., Pensalfini, A., Gou, D., Berk, A.J., Glabe, C.G., Nowick, J., Eisenberg, D.
Reference:	Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20913-8.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-microglobulin
Alternative Name:
Gene Name:
Sequence Length:	6
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P61769
Keyword(s):	Amyloidogenic peptide segment KDWSFY

Structure Information

PDB ID:	4E0K
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	0.97
R free:	0.131

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
nan	B	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
PE4	B	C16 H34 O8	354.44	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL	CCOCCOCCOCCOCCOCCOCCOCCO	PJWQOENWHPEPKI-UHFFFAOYSA-N
PE4	C	C16 H34 O8	354.44	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL	CCOCCOCCOCCOCCOCCOCCOCCO	PJWQOENWHPEPKI-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

F

Y

L

Y

T

A

K

N

X

S

A

14

Chain 2

1

A

F

Y

L

Y

T

A

K

N

X

S

A

14

Chain 3

1

A

F

Y

L

Y

T

A

K

N

X

S

A

14

Chain 4

1

A

F

Y

L

Y

T

A

K

N

X

S

A

14

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

FYLLYYT segment from human Beta 2 Microglobulin (62-68) displayed on 54-membered macrocycle scaffold

They designed out-of-register Beta-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register Beta-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.

Literature

PMID:	23213214
Author(s):	Liu, C., Zhao, M., Jiang, L., Cheng, P.N., Park, J., Sawaya, M.R., Pensalfini, A., Gou, D., Berk, A.J., Glabe, C.G., Nowick, J., Eisenberg, D.
Reference:	Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20913-8.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-microglobulin
Alternative Name:
Gene Name:
Sequence Length:	14
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P61769
Keyword(s):	Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)

Structure Information

PDB ID:	4E0L
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.7
R free:	0.257

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
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
MPD	A	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
HAO	B	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
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
HAO	C	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
MPD	C	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
HAO	D	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
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 2

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 3

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 4

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

SVQIVYK segment from human Tau (305-311) displayed on 54-membered macrocycle scaffold (form I)

They designed out-of-register Beta-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register Beta-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.

Literature

PMID:	23213214
Author(s):	Liu, C., Zhao, M., Jiang, L., Cheng, P.N., Park, J., Sawaya, M.R., Pensalfini, A., Gou, D., Berk, A.J., Glabe, C.G., Nowick, J., Eisenberg, D.
Reference:	Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20913-8.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Microtubule-associated protein tau
Alternative Name:
Gene Name:
Sequence Length:	14
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P10636
Keyword(s):	Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)

Structure Information

PDB ID:	4E0M
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.75
R free:	0.221

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
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF	B	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	B	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
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	B	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
4BF	C	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	C	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
MPD	C	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	C	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
4BF	D	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	D	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
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	D	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 2

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 3

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 4

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

SVQIVYK segment from human Tau (305-311) displayed on 54-membered macrocycle scaffold (form II)

They designed out-of-register Beta-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register Beta-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.

Literature

PMID:	23213214
Author(s):	Liu, C., Zhao, M., Jiang, L., Cheng, P.N., Park, J., Sawaya, M.R., Pensalfini, A., Gou, D., Berk, A.J., Glabe, C.G., Nowick, J., Eisenberg, D.
Reference:	Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20913-8.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Microtubule-associated protein tau
Alternative Name:
Gene Name:
Sequence Length:	14
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P10636
Keyword(s):	Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)

Structure Information

PDB ID:	4E0N
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.65
R free:	0.255

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
MPD	A	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	A	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
4BF	B	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	B	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
MPD	B	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	B	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
4BF	C	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	C	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
MPD	C	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF	D	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	D	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
MPD	D	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	D	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 2

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 3

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Chain 4

1

A

S

V

Q

I

V

Y

K

A

E

F

X

Y

K

14

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

SVQIVYK segment from human Tau (305-311) displayed on 54-membered macrocycle scaffold (form III)

They designed out-of-register Beta-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register Beta-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.

Literature

PMID:	23213214
Author(s):	Liu, C., Zhao, M., Jiang, L., Cheng, P.N., Park, J., Sawaya, M.R., Pensalfini, A., Gou, D., Berk, A.J., Glabe, C.G., Nowick, J., Eisenberg, D.
Reference:	Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20913-8.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Microtubule-associated protein tau
Alternative Name:
Gene Name:
Sequence Length:	14
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P10636
Keyword(s):	Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)

Structure Information

PDB ID:	4E0O
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.82
R free:	0.22899999

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
MPD	A	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF	B	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	B	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
MPD	B	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	B	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
4BF	C	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	C	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
MPD	C	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF	D	C9 H10 Br N O2	244.09	4-BROMO-L-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)Br	PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO	D	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
MPD	D	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PO4	D	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

H

D

C

V

N

I

6

Chain 2

1

E

Q

M

C

I

T

6

Chain 3

1

H

D

C

V

N

I

6

Chain 4

1

E

Q

M

C

I

T

6

Chain 5

1

H

D

C

V

N

I

6

Chain 6

1

E

Q

M

C

I

T

6

Chain 7

1

H

D

C

V

N

I

6

Chain 8

1

E

Q

M

C

I

T

6

Chain 9

1

H

D

C

V

N

I

6

Chain 10

1

E

Q

M

C

I

T

6

Chain 11

1

H

D

C

V

N

I

6

Chain 12

1

E

Q

M

C

I

T

6

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Fragment of human prion protein; Instead of forming a pair of sheets steric zipper reflective of amyloid, the DBPrP fragment assembled into distinct beta-sheet oligomers

The crystal structure of a fragment from human prion protein consisting of the disulfide-bond-linked portions of helices 2 and 3. Instead of forming a pair-of-sheets steric zipper structure characteristic of amyloid fibers, this fragment crystallized into a Beta-sheet-rich assembly of hexameric oligomers. This study reveals a never before observed structural motif for ordered protein aggregates and suggests a possible mechanism for self-propagation of misfolded conformations by such nonamyloid oligomers.

Literature

PMID:	23808589
Author(s):	Apostol, M.I., Perry, K., Surewicz, W.K.
Reference:	J Am Chem Soc. 2013 Jul 17;135(28):10202-5.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Prion protein
Alternative Name:
Gene Name:
Sequence Length:	6
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	4E1H
Amyloid Category:	Non-amyloid
Type:	Fibril
Global Stoichiometry:	Hetero 12-mer - A6B6
PDB Classification:	CELL CYCLE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.4
R free:	0.218

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CIT	G	C6 H8 O7	192.12	CITRIC ACID	C(C(=O)O)C(CC(=O)O)(C(=O)O)O	KRKNYBCHXYNGOX-UHFFFAOYSA-N
FE	G	Fe 3	55.85	FE (III) ION	[Fe+3]	VTLYFUHAOXGGBS-UHFFFAOYSA-N
CIT	I	C6 H8 O7	192.12	CITRIC ACID	C(C(=O)O)C(CC(=O)O)(C(=O)O)O	KRKNYBCHXYNGOX-UHFFFAOYSA-N
FE	I	Fe 3	55.85	FE (III) ION	[Fe+3]	VTLYFUHAOXGGBS-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Lysozyme in the presence of arginine

They report results on how heat transforms globular protein, lysozyme into building block of Beta-amyloids. Light scattering experiments showed formation of lower order associated species around 50-70?Â°C followed by rapid cooperativity to Beta-amyloid fibrils. crystallization drops set at higher temperatures either led to aggregates or spherulites. The latter possess an amorphous Beta-fibril rich core with thin crystalline needles projecting outwards. Diffraction of the crystalline outgrowths revealed novel dimers and trimers of lysozyme where individual chains were similar to monomer with marginal gain in Beta-sheet content. Overall this work concludes that heat induced weakly associated structures of lysozyme are the first step towards its amyloid formation.

Literature

PMID:	26926993
Author(s):	Sharma, P., Verma, N., Singh, P.K., Korpole, S., Ashish
Reference:	Sci Rep. 2016 Mar 1;6:22475.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Lysozyme C
Alternative Name:	1, 4-beta-N-acetylmuramidase C, Allergen Gal d IV
Gene Name:	LYZ
Sequence Length:	129
Species:	Gallus gallus
Mutation(s):	No
E.C. Number:	3.2.1.17
UniProt ID:	P00698
Keyword(s):	Lysozyme

Structure Information

PDB ID:	4EOF
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.83
R free:	0.24600000

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
ARG	A	C6 H15 N4 O2 1	175.21	ARGININE	C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N	ODKSFYDXXFIFQN-BYPYZUCNSA-O
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

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

I

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

I

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

The Structure of V122I Mutant Transthyretin in Complex with AG10

They report the development of AG10, a potent and selective kinetic stabilizer of TTR. AG10 prevents dissociation of V122I-TTR in serum samples obtained from patients with familial amyloid cardiomyopathy. In contrast to other TTR stabilizers currently in clinical trials, AG10 stabilizes V122I- and WT-TTR equally well and also exceeds their efficacy to stabilize WT and mutant TTR in whole serum.

Literature

PMID:	23716704
Author(s):	Penchala, S.C., Connelly, S., Wang, Y., Park, M.S., Zhao, L., Baranczak, A., Rappley, I., Vogel, H., Liedtke, M., Witteles, R.M., Powers, E.T., Reixach, N., Chan, W.K., Wilson, I.A., Kelly, J.W., Graef, I.A., Alhamadsheh, M.M.
Reference:	Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9992-7.

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):	V122I
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	4HIQ
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE BINDING PROTEIN/INHIBITOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.18
R free:	0.18600000

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
16V	A	C15 H17 F N2 O3	292.3	3-[3-(3,5-dimethyl-1H-pyrazol-4-yl)propoxy]-4-fluorobenzoic acid	Cc1c(c(n[nH]1)C)CCCOc2cc(ccc2F)C(=O)O	WBFUHHBPNXWNCC-UHFFFAOYSA-N
16V	B	C15 H17 F N2 O3	292.3	3-[3-(3,5-dimethyl-1H-pyrazol-4-yl)propoxy]-4-fluorobenzoic acid	Cc1c(c(n[nH]1)C)CCCOc2cc(ccc2F)C(=O)O	WBFUHHBPNXWNCC-UHFFFAOYSA-N

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

I

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

I

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

The Structure of V122I Mutant Transthyretin in Complex with Tafamidis

They report the development of AG10, a potent and selective kinetic stabilizer of TTR. AG10 prevents dissociation of V122I-TTR in serum samples obtained from patients with familial amyloid cardiomyopathy. In contrast to other TTR stabilizers currently in clinical trials, AG10 stabilizes V122I- and WT-TTR equally well and also exceeds their efficacy to stabilize WT and mutant TTR in whole serum.

Literature

PMID:	23716704
Author(s):	Penchala, S.C., Connelly, S., Wang, Y., Park, M.S., Zhao, L., Baranczak, A., Rappley, I., Vogel, H., Liedtke, M., Witteles, R.M., Powers, E.T., Reixach, N., Chan, W.K., Wilson, I.A., Kelly, J.W., Graef, I.A., Alhamadsheh, M.M.
Reference:	Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9992-7.

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):	V122I
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	4HIS
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE BINDING PROTEIN/INHIBITOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.2
R free:	0.172

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
3MI	A	C14 H7 Cl2 N O3	308.12	2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid	c1cc2c(cc1C(=O)O)oc(n2)c3cc(cc(c3)Cl)Cl	TXEIIPDJKFWEEC-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

V

F

E

R

C

E

L

A

R

T

L

K

R

L

G

M

D

G

Y

R

G

I

S

L

25

26

A

N

W

M

C

L

A

K

W

E

S

G

Y

N

T

R

A

T

N

Y

N

A

G

D

R

50

51

S

T

D

Y

G

I

F

Q

I

N

S

R

Y

W

C

N

D

G

K

T

P

G

A

V

N

75

76

A

C

H

L

S

C

S

A

L

Q

D

N

I

A

D

A

V

A

C

A

K

R

V

100

101

R

D

P

Q

G

I

R

A

W

V

A

W

R

N

R

C

Q

N

R

D

V

R

Q

Y

V

125

126

Q

G

C

G

V

130

Chain 2

1

K

V

F

E

R

C

E

L

A

R

T

L

K

R

L

G

M

D

G

Y

R

G

I

S

L

25

26

A

N

W

M

C

L

A

K

W

E

S

G

Y

N

T

R

A

T

N

Y

N

A

G

D

R

50

51

S

T

D

Y

G

I

F

Q

I

N

S

R

Y

W

C

N

D

G

K

T

P

G

A

V

N

75

76

A

C

H

L

S

C

S

A

L

Q

D

N

I

A

D

A

V

A

C

A

K

R

V

100

101

R

D

P

Q

G

I

R

A

W

V

A

W

R

N

R

C

Q

N

R

D

V

R

Q

Y

V

125

126

Q

G

C

G

V

130

Chain 3

1

Q

V

Q

L

Q

E

S

G

S

V

Q

A

G

S

L

R

L

S

C

E

A

S

25

26

G

L

S

T

V

M

A

W

F

R

Q

A

P

G

K

E

R

E

G

V

A

I

Y

50

51

T

G

D

G

F

P

Y

A

D

S

V

K

G

R

F

T

I

S

Q

D

N

A

K

N

75

76

R

M

Y

L

Q

M

N

S

L

E

P

E

D

T

A

M

Y

C

A

K

T

G

A

100

101

F

S

Y

G

S

L

W

M

S

R

A

Y

N

H

W

G

Q

G

T

Q

V

T

V

S

125

126

S

H

132

Chain 4

1

Q

V

Q

L

Q

E

S

G

S

V

Q

A

G

S

L

R

L

S

C

E

A

S

25

26

G

L

S

T

V

M

A

W

F

R

Q

A

P

G

K

E

R

E

G

V

A

I

Y

50

51

T

G

D

G

F

P

Y

A

D

S

V

K

G

R

F

T

I

S

Q

D

N

A

K

N

75

76

R

M

Y

L

Q

M

N

S

L

E

P

E

D

T

A

M

Y

C

A

K

T

G

A

100

101

F

S

Y

G

S

L

W

M

S

R

A

Y

N

H

W

G

Q

G

T

Q

V

T

V

S

125

126

S

H

132

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

The structure of the camelid antibody cAbHuL5 in complex with human lysozyme

They report the effects of the interaction of two camelid antibody fragments, generally called nanobodies, namely cAb-HuL5. cAb-HuL5 binds to the Alpha-domain, one of the two lobes of the native lysozyme structure. The binding of cAb-HuL5/cAb-HuL5G strongly inhibits fibril formation by the amyloidogenic variants; it does not, however, suppress the locally transient cooperative unfolding transitions, characteristic of these variants, in which the Beta-domain and the C-helix unfold and which represents key early intermediate species in the formation of amyloid fibrils.

Literature

PMID:	23919586
Author(s):	De Genst, E., Chan, P.H., Pardon, E., Hsu, S.T., Kumita, J.R., Christodoulou, J., Menzer, L., Chirgadze, D.Y., Robinson, C.V., Muyldermans, S., Matagne, A., Wyns, L., Dobson, C.M., Dumoulin, M.
Reference:	J Phys Chem B. 2013 Oct 24;117(42):13245-13258.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Lysozyme
Alternative Name:	1, 4-beta-N-acetylmuramidase C
Gene Name:	LYZ, LZM
Sequence Length:	130 , 132 , 132
Species:
Mutation(s):	No
E.C. Number:	3.2.1.17
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	4I0C
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Hetero 2-mer - AB
PDB Classification:	IMMUNE SYSTEM/HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.95
R free:	0.21899999

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
GOL	B	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

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

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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 in complex with CHF5074 at neutral pH

Structural evidence has been obtained by X-ray analysis for the native state stabilization of I84S TTR by two chemically distinct fibrillogenesis inhibitors. They fully prevent the acidic pH-induced protein conformational change as a result of a long-range stabilizing effect.

Literature

PMID:	23792159
Author(s):	Zanotti, G., Cendron, L., Folli, C., Florio, P., Imbimbo, B.P., Berni, R.
Reference:	FEBS Lett. 2013 Aug 2;587(15):2325-31.

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:	4I85
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	transport protein/inhibitor
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.67
R free:	0.23

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
H50	A	C16 H11 Cl2 F O2	325.16	1-(3',4'-dichloro-2-fluorobiphenyl-4-yl)cyclopropanecarboxylic acid	c1cc(c(cc1c2ccc(cc2F)C3(CC3)C(=O)O)Cl)Cl	LIYLTQQDABRNRX-UHFFFAOYSA-N
H50	B	C16 H11 Cl2 F O2	325.16	1-(3',4'-dichloro-2-fluorobiphenyl-4-yl)cyclopropanecarboxylic acid	c1cc(c(cc1c2ccc(cc2F)C3(CC3)C(=O)O)Cl)Cl	LIYLTQQDABRNRX-UHFFFAOYSA-N

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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 TTR variant I84S in complex with CHF5074 at acidic pH

Structural evidence has been obtained by X-ray analysis for the native state stabilization of I84S TTR by two chemically distinct fibrillogenesis inhibitors. They fully prevent the acidic pH-induced protein conformational change as a result of a long-range stabilizing effect.

Literature

PMID:	23792159
Author(s):	Zanotti, G., Cendron, L., Folli, C., Florio, P., Imbimbo, B.P., Berni, R.
Reference:	FEBS Lett. 2013 Aug 2;587(15):2325-31.

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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):	I84S
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	4I87
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	transport protein/inhibitor
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.69
R free:	0.21100000

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
H50	A	C16 H11 Cl2 F O2	325.16	1-(3',4'-dichloro-2-fluorobiphenyl-4-yl)cyclopropanecarboxylic acid	c1cc(c(cc1c2ccc(cc2F)C3(CC3)C(=O)O)Cl)Cl	LIYLTQQDABRNRX-UHFFFAOYSA-N
H50	B	C16 H11 Cl2 F O2	325.16	1-(3',4'-dichloro-2-fluorobiphenyl-4-yl)cyclopropanecarboxylic acid	c1cc(c(cc1c2ccc(cc2F)C3(CC3)C(=O)O)Cl)Cl	LIYLTQQDABRNRX-UHFFFAOYSA-N

Structure

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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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

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 in complex with diflunisal at acidic pH

Structural evidence has been obtained by X-ray analysis for the native state stabilization of I84S TTR by two chemically distinct fibrillogenesis inhibitors. They fully prevent the acidic pH-induced protein conformational change as a result of a long-range stabilizing effect.

Literature

PMID:	23792159
Author(s):	Zanotti, G., Cendron, L., Folli, C., Florio, P., Imbimbo, B.P., Berni, R.
Reference:	FEBS Lett. 2013 Aug 2;587(15):2325-31.

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:	4I89
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	transport protein/inhibitor
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.69
R free:	0.222

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
1FL	A	C13 H8 F2 O3	250.2	5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID	c1cc(c(cc1c2ccc(cc2F)F)C(=O)O)O	HUPFGZXOMWLGNK-UHFFFAOYSA-N
1FL	B	C13 H8 F2 O3	250.2	5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID	c1cc(c(cc1c2ccc(cc2F)F)C(=O)O)O	HUPFGZXOMWLGNK-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Lysozyme with Benzyl alcohol

They report results on how heat transforms globular protein, lysozyme into building block of Beta-amyloids. Light scattering experiments showed formation of lower order associated species around 50-70?Â°C followed by rapid cooperativity to Beta-amyloid fibrils. crystallization drops set at higher temperatures either led to aggregates or spherulites. The latter possess an amorphous Beta-fibril rich core with thin crystalline needles projecting outwards. Diffraction of the crystalline outgrowths revealed novel dimers and trimers of lysozyme where individual chains were similar to monomer with marginal gain in Beta-sheet content. Overall this work concludes that heat induced weakly associated structures of lysozyme are the first step towards its amyloid formation.

Literature

PMID:	26926993
Author(s):	Sharma, P., Verma, N., Singh, P.K., Korpole, S., Ashish
Reference:	Sci Rep. 2016 Mar 1;6:22475.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Lysozyme C
Alternative Name:	1, 4-beta-N-acetylmuramidase C, Allergen Gal d IV
Gene Name:	LYZ
Sequence Length:	129
Species:	Gallus gallus
Mutation(s):	No
E.C. Number:	3.2.1.17
UniProt ID:	P00698
Keyword(s):	Lysozyme C

Structure Information

PDB ID:	4II8
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.88
R free:	0.225

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
10	A	C7 H8 O	108.14	phenylmethanol	c1ccc(cc1)CO	WVDDGKGOMKODPV-UHFFFAOYSA-N
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
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

R

S

F

S

F

L

G

E

A

F

D

G

A

R

D

M

W

R

A

Y

S

D

M

25

26

R

E

A

N

Y

I

G

S

D

K

Y

F

H

A

R

G

N

Y

D

A

K

R

G

P

50

51

G

V

W

A

E

A

I

S

D

A

R

E

N

I

Q

R

F

G

H

G

A

E

75

76

D

S

L

A

D

Q

A

N

E

W

G

R

S

G

K

D

P

N

H

F

R

P

A

G

100

101

L

P

E

K

Y

105

Chain 2

1

M

R

S

F

S

F

L

G

E

A

F

D

G

A

R

D

M

W

R

A

Y

S

D

M

25

26

R

E

A

N

Y

I

G

S

D

K

Y

F

H

A

R

G

N

Y

D

A

K

R

G

P

50

51

G

V

W

A

E

A

I

S

D

A

R

E

N

I

Q

R

F

G

H

G

A

E

75

76

D

S

L

A

D

Q

A

N

E

W

G

R

S

G

K

D

P

N

H

F

R

P

A

G

100

101

L

P

E

K

Y

105

Chain 3

1

M

R

S

F

S

F

L

G

E

A

F

D

G

A

R

D

M

W

R

A

Y

S

D

M

25

26

R

E

A

N

Y

I

G

S

D

K

Y

F

H

A

R

G

N

Y

D

A

K

R

G

P

50

51

G

V

W

A

E

A

I

S

D

A

R

E

N

I

Q

R

F

G

H

G

A

E

75

76

D

S

L

A

D

Q

A

N

E

W

G

R

S

G

K

D

P

N

H

F

R

P

A

G

100

101

L

P

E

K

Y

105

Chain 4

1

M

R

S

F

S

F

L

G

E

A

F

D

G

A

R

D

M

W

R

A

Y

S

D

M

25

26

R

E

A

N

Y

I

G

S

D

K

Y

F

H

A

R

G

N

Y

D

A

K

R

G

P

50

51

G

V

W

A

E

A

I

S

D

A

R

E

N

I

Q

R

F

G

H

G

A

E

75

76

D

S

L

A

D

Q

A

N

E

W

G

R

S

G

K

D

P

N

H

F

R

P

A

G

100

101

L

P

E

K

Y

105

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Structure of human serum amyloid A1

They determined a structure of human SAA1 to understand its function and structural transition to amyloid, in two crystal forms, representing a prototypic member of the family.

Literature

PMID:	24706838
Author(s):	Lu, J., Yu, Y., Zhu, I., Cheng, Y., Sun, P.D.
Reference:	Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5189-94.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Serum amyloid A-1 protein
Alternative Name:
Gene Name:	SAA1
Sequence Length:	105
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P0DJI8
Keyword(s):	Serum amyloid A-1 protein

Structure Information

PDB ID:	4IP8
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	PROTEIN BINDING
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.19
R free:	0.256

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
P4C	A	C14 H28 O8	324.37	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL	C(COCCOCCOCCOCCOCCOCC=O)O	CTLLATPOKUEFSQ-UHFFFAOYSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
P4C	B	C14 H28 O8	324.37	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL	C(COCCOCCOCCOCCOCCOCC=O)O	CTLLATPOKUEFSQ-UHFFFAOYSA-N
SO4	B	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
P4C	C	C14 H28 O8	324.37	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL	C(COCCOCCOCCOCCOCCOCC=O)O	CTLLATPOKUEFSQ-UHFFFAOYSA-N
SO4	C	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
P4C	D	C14 H28 O8	324.37	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL	C(COCCOCCOCCOCCOCCOCC=O)O	CTLLATPOKUEFSQ-UHFFFAOYSA-N
SO4	D	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

H

R

S

F

S

F

L

G

E

A

F

D

G

A

R

D

M

W

25

26

R

A

Y

S

D

M

R

E

A

N

Y

I

G

S

D

K

Y

F

H

A

R

G

N

Y

D

50

51

A

K

R

G

P

G

V

W

A

E

A

I

S

D

A

R

E

N

I

Q

R

F

75

76

F

G

H

G

A

E

D

S

L

A

D

Q

A

N

E

W

G

R

S

G

K

D

P

N

100

101

H

F

R

P

A

G

L

P

E

K

Y

111

Chain 2

1

M

H

R

S

F

S

F

L

G

E

A

F

D

G

A

R

D

M

W

25

26

R

A

Y

S

D

M

R

E

A

N

Y

I

G

S

D

K

Y

F

H

A

R

G

N

Y

D

50

51

A

K

R

G

P

G

V

W

A

E

A

I

S

D

A

R

E

N

I

Q

R

F

75

76

F

G

H

G

A

E

D

S

L

A

D

Q

A

N

E

W

G

R

S

G

K

D

P

N

100

101

H

F

R

P

A

G

L

P

E

K

Y

111

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Structure of native human serum amyloid A1

They determined a structure of human SAA1 to understand its function and structural transition to amyloid. Native SAA1.1 exists as a hexamer, with subunits displaying a unique four-helix bundle fold stabilized by its long C-terminal tail. Structure-based mutational studies revealed two positive-charge clusters, near the center and apex of the hexamer, that are involved in SAA association with heparin. The binding of high-density lipoprotein involves only the apex region of SAA and can be inhibited by heparin. Peptide amyloid formation assays identified the N-terminal helices 1 and 3 as amyloidogenic peptides of SAA1.1.

Literature

PMID:	24706838
Author(s):	Lu, J., Yu, Y., Zhu, I., Cheng, Y., Sun, P.D.
Reference:	Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5189-94.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Serum amyloid A-1 protein
Alternative Name:
Gene Name:	SAA1
Sequence Length:	111
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P0DJI8
Keyword(s):	Serum amyloid A-1 protein

Structure Information

PDB ID:	4IP9
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	PROTEIN BINDING
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.5
R free:	0.258

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
P4C	A	C14 H28 O8	324.37	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL	C(COCCOCCOCCOCCOCCOCC=O)O	CTLLATPOKUEFSQ-UHFFFAOYSA-N
P4C	B	C14 H28 O8	324.37	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL	C(COCCOCCOCCOCCOCCOCC=O)O	CTLLATPOKUEFSQ-UHFFFAOYSA-N

Structure database of aggregation related proteins and peptides

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