CPAD 2.0

Entry	PDB ID	Protein Name	Species	Length	Mutation(s)	Class	Type	Method	Resolution (Å)	PMID
S-0001	1AMB	Amyloid-beta A4 protein	Homo sapiens	28	No	Amyloid	Peptide	SOLUTION NMR		7516706
S-0002	1AMC	Amyloid-beta A4 protein	Homo sapiens	28	No	Amyloid	Peptide	SOLUTION NMR		7516706
S-0003	1AML	Amyloid-beta A4 protein	Homo sapiens	40	No	Amyloid	Peptide	SOLUTION NMR		7588758
S-0004	1B0W	Immunoglobulin kappa variable 1-33	Homo sapiens	108	No	Amyloid	Protein	X-RAY DIFFRACTION	1.8	9818054
S-0005	1BA4	Amyloid-beta A4 protein	Homo sapiens	40	No	Amyloid	Peptide	SOLUTION NMR		9693002
S-0006	1BA6	Amyloid-beta A4 protein	Homo sapiens	40	No	Amyloid	Peptide	SOLUTION NMR		9737846
S-0007	1BJB	Amyloid-beta A4 protein	Homo sapiens	28	K16E	Amyloid	Peptide	SOLUTION NMR		10940222
S-0008	1BJC	Amyloid-beta A4 protein	Homo sapiens	28	K16F	Amyloid	Peptide	SOLUTION NMR		10940222
S-0009	1BM7	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.0	9789022
S-0010	1BMZ	Transthyretin	Homo sapiens	127	No	Amyloid	Protein	X-RAY DIFFRACTION	2.0	9789022
S-0011	1BRE	IMMUNOGLOBULIN LIGHT CHAIN PROTEIN (kappa I)	Homo sapiens	108	No	Amyloid	Fibril	X-RAY DIFFRACTION	2.0	7568160
S-0012	1BZD	Transthyretin	Homo sapiens	127	G6S	Non-amyloid	Protein	X-RAY DIFFRACTION	1.9	9818054
S-0013	1BZE	Transthyretin	Homo sapiens	127	T119M	Non-amyloid	Protein	X-RAY DIFFRACTION	1.8	9818054
S-0014	1CD0	Immunoglobulin lambda variable 6-57	Homo sapiens	111	No	Non-amyloid	Protein	X-RAY DIFFRACTION	1.9	10524280
S-0015	1CQM	30S ribosomal protein S6	Thermus thermophilus	101	E41A/E42I	Non-amyloid	Protein	X-RAY DIFFRACTION	1.65	10944185
S-0016	1CQN	30S ribosomal protein S6	Thermus thermophilus	101	E41A/E42I	Non-amyloid	Protein	X-RAY DIFFRACTION	2.1	10944185
S-0017	1DVQ	Transthyretin	Homo sapiens	124	No	Amyloid	Protein	X-RAY DIFFRACTION	2.0	10742177
S-0018	1DVS	Transthyretin	Homo sapiens	124	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.0	10742177
S-0019	1DVT	Transthyretin	Homo sapiens	124	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.9	10742177
S-0020	1DVU	Transthyretin	Homo sapiens	124	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.9	10742177
S-0021	1DVX	Transthyretin	Homo sapiens	124	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.0	10742177
S-0022	1DVY	Transthyretin	Homo sapiens	124	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.9	10742177
S-0023	1DVZ	Transthyretin	Homo sapiens	124	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.9	10742177
S-0024	1EK3	Immunoglobulin kappa variable 4-1	Homo sapiens	114	No	Amyloid	Protein	X-RAY DIFFRACTION	1.9
S-0025	1F0V	RNase A		124 , 2 , 2 , 2 , 2	No	Amyloid	Protein	X-RAY DIFFRACTION	1.7	11224563
S-0026	1FH2	Transthyretin	Homo sapiens	127	V30M/T119M	Non-amyloid	Protein	X-RAY DIFFRACTION	1.8	11243784
S-0027	1FHN	Transthyretin	Homo sapiens	127	T119M	Non-amyloid	Protein	X-RAY DIFFRACTION	1.75	11243784
S-0028	1F86	Transthyretin	Homo sapiens	127	T119M	Non-amyloid	Protein	X-RAY DIFFRACTION	1.75	11243784
S-0029	1G96	Cystatin-C	Homo sapiens	120	No	Amyloid	Protein	X-RAY DIFFRACTION	2.5	11276250
S-0030	1GKO	Transthyretin	Homo sapiens	127	F87M/L110M	Amyloid	Protein	X-RAY DIFFRACTION	2.1	11560492

Structure

Press 'p' to pause
View interactive contact network

Sequence & Sec. Str.

Chain 1

1

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

F

A

E

D

V

G

25

26

S

N

K

28

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

Charged residues and Proline are highlighed in blue.

Description

SOLUTION STRUCTURE OF RESIDUES 1-28 OF THE AMYLOID BETA-PEPTIDE

Solution structure of residues 1-28 of the amyloid Beta-peptide was determined using nuclear magnetic resonance spectroscopy. In membrane-like media, the peptide folds to form a predominately Alpha-helical structure with a bend centered at residue 12. An Alpha-helix-->Beta-sheet conversion may occur during the early stages of amyloid formation in Alzheimer's disease.

Literature

PMID:	7516706
Author(s):	Talafous, J., Marcinowski, K.J., Klopman, G., Zagorski, M.G.
Reference:	Biochemistry. 1994 Jun 28;33(25):7788-96

Download

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

Protein Information

Protein Name:	Amyloid-beta A4 protein
Alternative Name:	ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:	APP, A4, AD1
Sequence Length:	28
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P05067
Keyword(s):	AMYLOID BETA-PEPTIDE

Structure Information

PDB ID:	1AMB
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:	Monomer - A
PDB Classification:	PROTEINASE INHIBITOR(TRYPSIN)
Method:	SOLUTION NMR
Resolution (Å):
R free:

Structure

Press 'p' to pause
View interactive contact network

Sequence & Sec. Str.

Chain 1

1

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

F

A

E

D

V

G

25

26

S

N

K

G

A

I

G

L

M

V

G

V

40

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

Charged residues and Proline are highlighed in blue.

Description

SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED AMYLOID BETA-PEPTIDE (1-40)

The solution structure of ABeta(1-40)Met(O), the methionine-oxidized form of ABeta(1-40), has been investigated. Oxidation of Met35 may have implications in the aetiology of Alzheimer's disease. Experiments strongly suggest the presence of a helical region between residues 16 and 24 in ABeta(1-40)Met(O). Oxidation of Met35 causes a local and selective disruption of helix 2. In addition to this helix-coil rearrangement in aqueous micelles, the CD data show that oxidation inhibits a coil-to-Beta-sheet transition in water.

Literature

PMID:	9737846
Author(s):	Watson, A.A., Fairlie, D.P., Craik, D.J.
Reference:	Biochemistry. 1998 Sep 15;37(37):12700-6

Download

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

Protein Information

Protein Name:	Amyloid-beta A4 protein
Alternative Name:	ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:	APP, A4, AD1
Sequence Length:	40
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P05067
Keyword(s):	AMYLOID BETA-PEPTIDE

Structure Information

PDB ID:	1BA6
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:	Monomer - A
PDB Classification:	GLYCOPROTEIN
Method:	SOLUTION NMR
Resolution (Å):
R free:

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
SME	A	C5 H11 N O3 S	165.21	METHIONINE SULFOXIDE	C[S@@](=O)CC[C@@H](C(=O)O)N	QEFRNWWLZKMPFJ-ZXPFJRLXSA-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

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

Inhibiting transthyretin conformational changes that lead to amyloid fibril formation

#Ligand: FLUFENAMIC ACID (2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID)# Flufenamic acid (Flu) inhibits the conformational changes of TTR associated with amyloid fibril formation. The crystal structure of TTR complexed with Flu demonstrates that Flu mediates intersubunit hydrophobic interactions and intersubunit hydrogen bonds that stabilize the normal tetrameric fold of TTR.

Literature

PMID:	9789022
Author(s):	Peterson, S.A., Klabunde, T., Lashuel, H.A., Purkey, H., Sacchettini, J.C., Kelly, J.W.
Reference:	Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12956-60

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):	PROTEIN (TRANSTHYRETIN)

Structure Information

PDB ID:	1BM7
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	SIGNALING PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.0
R free:	0.251

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
FLF	A	C14 H10 F3 N O2	281.23	2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID	c1ccc(c(c1)C(=O)O)Nc2cccc(c2)C(F)(F)F	LPEPZBJOKDYZAD-UHFFFAOYSA-N
FLF	B	C14 H10 F3 N O2	281.23	2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID	c1ccc(c(c1)C(=O)O)Nc2cccc(c2)C(F)(F)F	LPEPZBJOKDYZAD-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

Q

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

124

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

Q

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

124

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

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH RESVERATROL

Resveratrol (RESV, trans-3,4?,5-trihydroxystilbene) is an antioxidant present in red wine and grape juice that has been shown to inhibit platelet aggregation and is implicated in the prevention of congestive heart failure due to coronary thrombosis. The X-ray structure of the TTRâ€“RESV complex shows that the inhibitor fits well into the T4 binding site, while maintaining its minimum energy conformation. Ligandâ€“protein interactions are dominated by non-polar contacts mediated by the stilbene moiety, which is stacked between the hydrophobic side chains of Lys 15, Leu 17, Ala 108, Leu 110, Ser 117, Thr 119 and Val 121.

Literature

PMID:	10742177
Author(s):	Klabunde, T., Petrassi, H.M., Oza, V.B., Raman, P., Kelly, J.W., Sacchettini, J.C.
Reference:	Nat Struct Biol. 2000 Apr;7(4):312-21

Download

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

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	124
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	TRANSTHYRETIN

Structure Information

PDB ID:	1DVS
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.0
R free:	0.22699999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
STL	A	C14 H12 O3	228.24	RESVERATROL	c1cc(ccc1C=Cc2cc(cc(c2)O)O)O	LUKBXSAWLPMMSZ-OWOJBTEDSA-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

Q

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

124

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

Q

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

124

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

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH FLURBIPROFEN

Flurbiprofen (FLP), a biphenyl-based NSAID functionalized with a carboyxlate group, has been found to inhibit TTR fibril formation and represents another potential lead compound for the structure-based ligand design for TTR-associated human amyloid diseases. FLP binds to TTR in a conformation near its calculated lowest-energy conformation. The biaryl system of FLP was flanked on both sides by the hydrophobic side chains of Lys 15, Leu 17, Ala 108, Leu 110, Ser 117, Thr 119, and Val 121. The interactions between FLP and TTR are augmented by an ionic interaction between the carboxylate group of FLP and a Lys 15 from the protein.

Literature

PMID:	10742177
Author(s):	Klabunde, T., Petrassi, H.M., Oza, V.B., Raman, P., Kelly, J.W., Sacchettini, J.C.
Reference:	Nat Struct Biol. 2000 Apr;7(4):312-21

Download

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

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	124
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	TRANSTHYRETIN

Structure Information

PDB ID:	1DVT
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.22

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
FLP	A	C15 H13 F O2	244.26	FLURBIPROFEN	C[C@@H](c1ccc(c(c1)F)c2ccccc2)C(=O)O	SYTBZMRGLBWNTM-JTQLQIEISA-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

Q

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

124

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

Q

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

124

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

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH DIBENZOFURAN-4,6-DICARBOXYLIC ACID

The X-ray structure of TTRâ€“DDBF shows the DDBF binds, as predicted, to both hormone binding cavities at the dimer-dimer interface of TTR. The tricyclyic ring system was located between residues Lys 15, Val 17 and Ala 108 from two adjacent TTR subunits, stretching across the outer region of the hormone binding cavity from HBP-1 to HBP-1'. One of the carboxylate groups of DDBF formed hydrogen bond interactions with the amino groups of Lys 15 from two adjacent TTR subunits. Ser 117 and Thr 119 do not undergo the conformational changes observed in most other TTRâ€“inhibitor complexes.

Literature

PMID:	10742177
Author(s):	Klabunde, T., Petrassi, H.M., Oza, V.B., Raman, P., Kelly, J.W., Sacchettini, J.C.
Reference:	Nat Struct Biol. 2000 Apr;7(4):312-21

Download

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

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	124
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	TRANSTHYRETIN

Structure Information

PDB ID:	1DVU
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.22

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
DBF	B	C14 H8 O5	256.21	DIBENZOFURAN-4,6-DICARBOXYLIC ACID	c1cc2c3cccc(c3oc2c(c1)C(=O)O)C(=O)O	HBBGSNOHAGNQRQ-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

Q

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

124

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

Q

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

124

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

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH DICLOFENAC

DIC bind TTR and inhibit TTR amyloid formation is elucidated. Metabolic stability, significant oral absorption, and low toxicity have already been proven for the drug in numerous clinical trials. Due to the superior gastrointestinal tolerability of DIC it is more likely to have clinical utility as a chemotherapy treatment of human TTR-associated amyloid diseases. TTRâ€“DIC complex showed that the inhibitor has good steric complementarity with the T4 binding site. The active, propeller-like conformation of the inhibitor bound to TTR was close to the lowest energy conformation of the compound. Due to the two-fold symmetry of the binding cavity, DIC was found in two binding modes (DIC1 and DIC2) that are related by a 180Â° rotation along the hormone binding channel. DIC forms interactions with residues Lys 15, Leu 17, Ala 108, Leu 110, Ser 117, Thr 119, and Val 121 of two adjacent TTR subunits, thus mediating several intersubunit interactions. SAR demonstrated that the hydrogen bond between the carboxylate group of the inhibitor and Thr 119 contributes to diclofenac's affinity for TTR and its potency as a fibril formation inhibitor.

Literature

PMID:	10742177
Author(s):	Klabunde, T., Petrassi, H.M., Oza, V.B., Raman, P., Kelly, J.W., Sacchettini, J.C.
Reference:	Nat Struct Biol. 2000 Apr;7(4):312-21

Download

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

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	124
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	TRANSTHYRETIN

Structure Information

PDB ID:	1DVX
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.0
R free:	0.215

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
DIF	B	C14 H11 Cl2 N O2	296.15	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID	c1ccc(c(c1)CC(=O)O)Nc2c(cccc2Cl)Cl	DCOPUUMXTXDBNB-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

Q

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

124

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

Q

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

124

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

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE OF TRANSTHYRETIN IN COMPLEX WITH N-(M-TRIFLUOROMETHYLPHENYL) PHENOXAZINE-4,6-DICARBOXYLIC ACID

N-phenyl phenoxazine-4,6-dicarboxylate was constructed computationally and modeled to completely fill the available inner cavity of the hormone binding sites. PHENOX stabilizes the native TTR tetramer thus inhibiting the formation of amyloid fibrils. The crystal structure of TTR in complex with PHENOX shows the N-phenyl-substituted phenoxazine bound in its low energy conformation, with the planes of the distal phenyl ring and the tricyclic ring system almost orthogonal to each other. Extensive van der Waals interactions with the protein are observed, including those with the side chains of Thr 106, Lys 15 and Leu 17 from two adjacent subunits. The trifluoromethyl group of PHENOX does not bind as deep in the halogen binding pocket as the corresponding substituent of flufenamic acid. . However, PHENOX binds deep enough to displace an ordered water molecule found in the HBP-3 of apo-TTR.

Literature

PMID:	10742177
Author(s):	Klabunde, T., Petrassi, H.M., Oza, V.B., Raman, P., Kelly, J.W., Sacchettini, J.C.
Reference:	Nat Struct Biol. 2000 Apr;7(4):312-21

Download

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

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	124
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	TRANSTHYRETIN

Structure Information

PDB ID:	1DVY
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.203

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
BPD	A	C21 H12 F3 N O5	415.32	N-(M-TRIFLUOROMETHYLPHENYL) PHENOXAZINE-4,6-DICARBOXYLIC ACID	c1cc(cc(c1)N2c3cccc(c3Oc4c2cccc4C(=O)O)C(=O)O)C(F)(F)F	NQOOJFXBGLOGTC-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

Q

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

124

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

Q

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

124

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

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH O-TRIFLUOROMETHYLPHENYL ANTHRANILIC ACID

The crystal structure of the TTRâ€“oFLU complex shows that oFLU binds deep in the two funnel-shaped hormone-binding cavities located at the dimerâ€“dimer interface of TTR. The carboxylate-substituted phenyl ring is positioned near the entry of the binding channel. the trifluoromethyl-substituted phenyl ring of oFLU fits well into HBP-3 and HBP-3?. Both, the phenyl ring and the CF3 group, show favorable van der Waals packing with the side chains of Ala 108, Ala 109, Leu 110, Ser 117 and Thr 119 from two adjacent TTR subunits, thus contributing to the stabilization of the tetrameric structure of TTR. However, a slight rotation of the carboxylate-substituted phenyl ring of the inhibitor prohibits the carboxylate group of oFLU from forming a direct electrostatic interaction with the amino group of Lys 15, as observed for the TTRâ€“FLU structure. Instead, in the TTRâ€“oFLU complex, a hydrogen bond between these groups was mediated via an ordered water molecule.

Literature

PMID:	10742177
Author(s):	Klabunde, T., Petrassi, H.M., Oza, V.B., Raman, P., Kelly, J.W., Sacchettini, J.C.
Reference:	Nat Struct Biol. 2000 Apr;7(4):312-21

Download

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

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	124
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	TRANSTHYRETIN

Structure Information

PDB ID:	1DVZ
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.2

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
OFL	A	C14 H10 F3 N O2	281.23	O-TRIFLUOROMETHYLPHENYL ANTHRANILIC ACID	c1ccc(c(c1)C(=O)O)Nc2ccccc2C(F)(F)F	ONKHJNFXJDEMNQ-UHFFFAOYSA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

D

I

V

M

T

Q

S

P

D

S

L

A

V

S

P

G

E

R

A

T

I

N

C

K

S

25

26

S

Q

N

L

D

S

F

D

T

N

T

L

A

W

Y

Q

K

P

G

Q

P

50

51

K

L

I

Y

W

A

S

R

E

S

G

V

P

D

R

F

S

G

S

G

S

G

T

75

76

D

F

T

L

T

I

S

L

Q

A

E

D

V

A

V

Y

C

Q

Y

S

T

100

101

P

T

F

G

T

K

V

E

I

K

R

114

Chain 2

1

D

I

V

M

T

Q

S

P

D

S

L

A

V

S

P

G

E

R

A

T

I

N

C

K

S

25

26

S

Q

N

L

D

S

F

D

T

N

T

L

A

W

Y

Q

K

P

G

Q

P

50

51

K

L

I

Y

W

A

S

R

E

S

G

V

P

D

R

F

S

G

S

G

S

G

T

75

76

D

F

T

L

T

I

S

L

Q

A

E

D

V

A

V

Y

C

Q

Y

S

T

100

101

P

T

F

G

T

K

V

E

I

K

R

114

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

Charged residues and Proline are highlighed in blue.

Description

The Structure of Amyloidogenic Kappa-4 Immunoglobulin VL

The Structure of Amyloidogenic Kappa-4 Immunoglobulin VL, REC

Literature

PMID:
Author(s):	Pokkuluri, P.R., Huang, D.-B., Raffen, R., Stevens, F.J., Schiffer, M.
Reference:

Download

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

Protein Information

Protein Name:	Immunoglobulin kappa variable 4-1
Alternative Name:	Ig kappa chain V-IV region B17, Ig kappa chain V-IV region JI, Ig kappa chain V-IV region Len, Ig kappa chain V-IV region STH
Gene Name:	IGKV4-1
Sequence Length:	114
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P06312
Keyword(s):	KAPPA-4 IMMUNOGLOBULIN LIGHT CHAIN VL

Structure Information

PDB ID:	1EK3
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.237

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
CL	A	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

K

E

T

A

K

F

E

R

Q

H

M

D

S

T

S

A

S

N

Y

25

26

C

N

Q

M

K

S

R

N

L

T

K

D

R

C

K

P

V

N

T

F

V

H

E

S

50

51

L

A

D

V

Q

A

V

C

S

Q

K

N

V

A

C

K

N

G

Q

T

N

C

Y

Q

S

75

76

Y

S

T

M

S

I

T

D

C

R

E

T

G

S

K

Y

P

N

C

A

Y

K

T

100

101

Q

A

N

K

H

I

V

A

C

E

G

N

P

Y

V

P

V

H

F

D

A

S

V

124

Chain 2

1

K

E

T

A

K

F

E

R

Q

H

M

D

S

T

S

A

S

N

Y

25

26

C

N

Q

M

K

S

R

N

L

T

K

D

R

C

K

P

V

N

T

F

V

H

E

S

50

51

L

A

D

V

Q

A

V

C

S

Q

K

N

V

A

C

K

N

G

Q

T

N

C

Y

Q

S

75

76

Y

S

T

M

S

I

T

D

C

R

E

T

G

S

K

Y

P

N

C

A

Y

K

T

100

101

Q

A

N

K

H

I

V

A

C

E

G

N

P

Y

V

P

V

H

F

D

A

S

V

124

Chain 3

1

K

E

T

A

K

F

E

R

Q

H

M

D

S

T

S

A

S

N

Y

25

26

C

N

Q

M

K

S

R

N

L

T

K

D

R

C

K

P

V

N

T

F

V

H

E

S

50

51

L

A

D

V

Q

A

V

C

S

Q

K

N

V

A

C

K

N

G

Q

T

N

C

Y

Q

S

75

76

Y

S

T

M

S

I

T

D

C

R

E

T

G

S

K

Y

P

N

C

A

Y

K

T

100

101

Q

A

N

K

H

I

V

A

C

E

G

N

P

Y

V

P

V

H

F

D

A

S

V

124

Chain 4

1

K

E

T

A

K

F

E

R

Q

H

M

D

S

T

S

A

S

N

Y

25

26

C

N

Q

M

K

S

R

N

L

T

K

D

R

C

K

P

V

N

T

F

V

H

E

S

50

51

L

A

D

V

Q

A

V

C

S

Q

K

N

V

A

C

K

N

G

Q

T

N

C

Y

Q

S

75

76

Y

S

T

M

S

I

T

D

C

R

E

T

G

S

K

Y

P

N

C

A

Y

K

T

100

101

Q

A

N

K

H

I

V

A

C

E

G

N

P

Y

V

P

V

H

F

D

A

S

V

124

Chain 5



	1	C	G	2

Chain 6



	1	C	G	2

Chain 7



	1	C	G	2

Chain 8



	1	C	G	2

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

Charged residues and Proline are highlighed in blue.

Description

A domain-swapped RNase A dimer with implications for amyloid formation

Bovine pancreatic ribonuclease (RNase A) forms two types of dimers (a major and a minor component) upon concentration in mild acid. The minor dimer forms by swapping its N-terminal Alpha-helix with that of an identical molecule. The major dimer forms by swapping its C-terminal Beta-strand. This feature permits RNase A to form tightly bonded higher oligomers. The hinge loop of the major dimer, connecting the swapped Beta-strand to the protein core, resembles a short segment of the polar zipper.

Literature

PMID:	11224563
Author(s):	Liu, Y.S., Gotte, G., Libonati, M., Eisenberg, D.S.
Reference:	Nat Struct Biol. 2001 Mar;8(3):211-4

Download

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

Protein Information

Protein Name:	RNase A
Alternative Name:	RNase 1, RNase A
Gene Name:	RNASE1, RNS1
Sequence Length:	124 , 2 , 2 , 2 , 2
Species:
Mutation(s):	No
E.C. Number:	3.1.27.5
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	1F0V
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Monomer - A
PDB Classification:	hydrolase/DNA
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.7
R free:	0.213

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
GOL	A	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PO4	A	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PO4	B	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PO4	C	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PO4	P	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

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

M

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

M

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

Transthyretin stability as a key factor in amyloidogenesis

The main interactions between two monomers in a dimer result from H-bonds. The non-crystallographic TTR monomers are closer in the case of this non-amyloidogenic TTR variant compared to amyloidogenic TTR Val30Met,

Literature

PMID:	11243784
Author(s):	Sebastiao, M.P., Lamzin, V., Saraiva, M.J., Damas, A.M.
Reference:	J Mol Biol. 2001 Mar 2;306(4):733-44

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):	T119M
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	1F86
Amyloid Category:	Non-amyloid
Type:	Protein
Global Stoichiometry:	Homo 2-mer -Â A2
PDB Classification:	TRANSPORT PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.75
R free:	0.18

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
T44	A	C15 H11 I4 N O4	776.87	3,5,3',5'-TETRAIODO-L-THYRONINE	c1c(cc(c(c1I)Oc2cc(c(c(c2)I)O)I)I)C[C@@H](C(=O)O)N	XUIIKFGFIJCVMT-LBPRGKRZSA-N
T44	B	C15 H11 I4 N O4	776.87	3,5,3',5'-TETRAIODO-L-THYRONINE	c1c(cc(c(c1I)Oc2cc(c(c(c2)I)O)I)I)C[C@@H](C(=O)O)N	XUIIKFGFIJCVMT-LBPRGKRZSA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

S

P

G

K

P

R

L

V

G

P

M

D

A

S

V

E

G

V

R

25

26

A

L

D

F

A

V

G

E

Y

N

K

A

S

N

D

M

Y

H

S

R

A

L

Q

V

50

51

R

A

R

K

Q

I

V

A

G

V

N

Y

F

L

D

V

E

L

G

R

T

C

T

K

75

76

T

Q

P

N

L

D

N

C

P

F

H

D

Q

P

H

L

K

R

K

A

F

C

S

F

Q

100

101

I

Y

A

V

P

W

Q

G

T

M

T

L

S

K

S

T

C

Q

D

A

120

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

Charged residues and Proline are highlighed in blue.

Description

Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping

human cystatin C protein refolds to produce very tight two-fold symmetric dimers while retaining the secondary structure of the monomeric form. The dimerization occurs through three-dimensional domain swapping, a mechanism for forming oligomeric proteins. The tendency of human cystatin C to dimerize and suggests a mechanism for its aggregation in the brain arteries of elderly people with amyloid angiopathy.

Literature

PMID:	11276250
Author(s):	Janowski, R., Kozak, M., Jankowska, E., Grzonka, Z., Grubb, A., Abrahamson, M., Jaskolski, M.
Reference:	Nat Struct Biol. 2001 Apr;8(4):316-20

Download

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

Protein Information

Protein Name:	Cystatin-C
Alternative Name:	Cystatin-3, Gamma-trace, Neuroendocrine basic polypeptide, Post-gamma-globulin
Gene Name:	CST3
Sequence Length:	120
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P01034
Keyword(s):	CYSTATIN C

Structure Information

PDB ID:	1G96
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	hydrolase inhibitor
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.5
R free:	0.249

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

Structure database of aggregation related proteins and peptides

Displaying 1 to 30 records out of 565 records fetched.

PMID:	7588758
Author(s):	Sticht, H., Bayer, P., Willbold, D., Dames, S., Hilbich, C., Beyreuther, K., Frank, R.W., Rosch, P.
Reference:	Eur J Biochem. 1995 Oct 1;233(1):293-8

PMID:	9818054
Author(s):	Schormann, N., Murrell, J.R., Benson, M.D.
Reference:	Amyloid. 1998 Sep;5(3):175-87