CPAD 2.0

Entry	PDB ID	Protein Name	Species	Length	Mutation(s)	Class	Type	Method	Resolution (Å)	PMID
S-0451	5MVG	Immunoglobin light chain dimer M7	Homo sapiens	214	No	Non-amyloid	Protein	X-RAY DIFFRACTION	2.2	29196671
S-0452	5MY4	Amyloid-beta		219 , 231 , 10	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.21	28623233
S-0453	5MYK	Amyloid-beta		219 , 231 , 16	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.6	28623233
S-0454	5MYO	Amyloid-beta		219 , 228 , 219 , 228 , 10	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.59	28623233
S-0455	5MYX	Amyloid-beta		219 , 248 , 219 , 248 , 16 , 16	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.49	28623233
S-0456	5O3L	Microtubule-associated protein tau	Homo sapiens	73	No	Amyloid	Fibril	ELECTRON MICROSCOPY	3.4	28678775
S-0457	5O3O	Microtubule-associated protein tau	Homo sapiens	73	No	Amyloid	Fibril	ELECTRON MICROSCOPY	3.5	28678775
S-0458	5O3T	Microtubule-associated protein tau	Homo sapiens	73	No	Amyloid	Fibril	ELECTRON MICROSCOPY	3.4	28678775
S-0459	5ONP	Amyloid-beta		316 , 5	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.34	30403288
S-0460	5ONQ	Amyloid-beta		316 , 5	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.17	30403288
S-0461	5ONR	Amyloid-beta		316 , 3	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.39	30403288
S-0462	5OQV	Amyloid-beta A4 protein	Homo sapiens	42	No	Amyloid	Fibril	ELECTRON MICROSCOPY	4.0	28882996
S-0463	5T93	Immunoglobulin light chain variable domain AL-T05	Homo sapiens	110	No	Amyloid	Protein	X-RAY DIFFRACTION	1.9	28074646
S-0464	5TTR	Transthyretin	Homo sapiens	127	L55P	Amyloid	Protein	X-RAY DIFFRACTION	2.7	9733771
S-0465	5TXD	Amyloid-beta A4 protein	Homo sapiens	6	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.45	29349888
S-0466	5TXH	Amyloid-beta	Homo sapiens	6	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.45	29349888
S-0467	5TXJ	Amyloid-beta	Homo sapiens	6	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.13	29349888
S-0468	5UGK	Synthetic	synthetic construct	7	No	Amyloid	Fibril	SOLID-STATE NMR		28566494
S-0469	5UHR	Islet amyloid polypeptide (IAPP)	Homo sapiens	14	No	Non-amyloid	Fibril	X-RAY DIFFRACTION	1.8	28661686
S-0470	5V5B	Microtubule-associated protein tau	Homo sapiens	10	No	Amyloid	Fibril	ELECTRON CRYSTALLOGRAPHY	1.5	29359764
S-0471	5V5C	Microtubule-associated protein tau	Homo sapiens	6	No	Amyloid	Fibril	ELECTRON CRYSTALLOGRAPHY	1.25	29359764
S-0472	5V63	Amyloid-beta	synthetic construct	17	No	Amyloid	Peptide	X-RAY DIFFRACTION	2.0909999999999997	28683555
S-0473	5V64	Amyloid-beta	synthetic construct	16	No	Amyloid	Peptide	X-RAY DIFFRACTION	2.02	28683555
S-0474	5V65	Amyloid-beta	synthetic construct	16	No	Amyloid	Peptide	X-RAY DIFFRACTION	2.52	28683555
S-0475	5V7Z	RIP1/RIP3 Necrosome		15 , 18 , 15 , 18 , 15 , 18 , 15 , 18	No	Amyloid	Fibril	SOLID-STATE NMR		29681455
S-0476	5VF1	Amyloid-beta	Homo sapiens	16	No	Non-amyloid	Fibril	X-RAY DIFFRACTION	2.1	28598147
S-0477	5VOS	Amyloid-beta A4 protein	Homo sapiens	11	No	Amyloid	Fibril	ELECTRON CRYSTALLOGRAPHY	1.42	29282295
S-0478	5VZY	Amyloid-beta		15 , 220 , 219	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.32	27996029
S-0479	5W3P	Amyloid-beta		222 , 212 , 18	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.92	28830506
S-0480	5W4H	Amyloid-beta	Homo sapiens	16	No	Amyloid	Peptide	X-RAY DIFFRACTION	1.72	29028351

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

S

E

L

T

Q

D

P

A

V

S

V

A

L

G

Q

T

V

K

I

T

C

Q

G

D

25

26

S

L

R

M

Y

A

S

W

Y

Q

K

P

A

Q

A

P

V

L

V

I

Y

A

E

50

51

K

N

R

P

S

G

I

P

D

R

F

S

A

S

G

S

T

A

S

L

T

I

T

75

76

G

A

Q

A

E

D

E

A

D

Y

C

N

S

R

D

N

S

G

D

H

L

V

F

G

100

101

G

T

K

L

T

V

L

G

Q

P

K

A

P

S

V

T

L

F

P

S

E

125

126

E

L

Q

A

N

K

A

T

L

V

C

L

I

S

D

F

Y

P

G

A

V

T

V

A

W

150

151

K

A

D

S

P

V

K

A

G

V

E

T

P

S

K

Q

S

N

K

Y

A

175

176

A

S

Y

L

S

L

T

P

E

Q

W

K

S

H

R

S

Y

S

C

Q

V

T

H

E

200

201

G

S

T

V

E

K

T

V

A

P

T

E

C

S

214

Chain 2

1

S

E

L

T

Q

D

P

A

V

S

V

A

L

G

Q

T

V

K

I

T

C

Q

G

D

25

26

S

L

R

M

Y

A

S

W

Y

Q

K

P

A

Q

A

P

V

L

V

I

Y

A

E

50

51

K

N

R

P

S

G

I

P

D

R

F

S

A

S

G

S

T

A

S

L

T

I

T

75

76

G

A

Q

A

E

D

E

A

D

Y

C

N

S

R

D

N

S

G

D

H

L

V

F

G

100

101

G

T

K

L

T

V

L

G

Q

P

K

A

P

S

V

T

L

F

P

S

E

125

126

E

L

Q

A

N

K

A

T

L

V

C

L

I

S

D

F

Y

P

G

A

V

T

V

A

W

150

151

K

A

D

S

P

V

K

A

G

V

E

T

P

S

K

Q

S

N

K

Y

A

175

176

A

S

Y

L

S

L

T

P

E

Q

W

K

S

H

R

S

Y

S

C

Q

V

T

H

E

200

201

G

S

T

V

E

K

T

V

A

P

T

E

C

S

214

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

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of non-amyloidogenic light chain dimer M7

Eight amyloidogenic LCs were selected as responsible for severe cardiac symptoms in patients; five non-amyloidogenic LCs were isolated from patients affected by multiple myeloma. They showed that low fold stability and high protein dynamics correlate with amyloidogenic LCs, while hydrophobicity, structural rearrangements and nature of the LC dimeric association interface do not appear to play a significant role in defining amyloid propensity.

Literature

PMID:	29196671
Author(s):	Oberti, L., Rognoni, P., Barbiroli, A., Lavatelli, F., Russo, R., Maritan, M., Palladini, G., Bolognesi, M., Merlini, G., Ricagno, S.
Reference:	Sci Rep. 2017 Dec 1;7(1):16809.

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

Protein Information

Protein Name:	Immunoglobin light chain dimer M7
Alternative Name:
Gene Name:
Sequence Length:	214
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	light chain dimer

Structure Information

PDB ID:	5MVG
Amyloid Category:	Non-amyloid
Type:	Protein
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.2
R free:	0.239

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

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

D

V

M

T

Q

T

P

L

S

L

P

V

S

L

G

D

Q

A

S

I

S

C

R

S

25

26

S

Q

S

L

V

H

S

D

G

N

T

Y

L

H

W

Y

L

Q

K

P

G

Q

S

P

K

50

51

L

I

Y

K

V

S

N

R

F

S

G

V

P

D

R

F

S

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

V

E

A

E

D

L

G

V

Y

F

C

S

Q

S

T

H

V

P

100

101

P

T

F

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 2

1

E

V

K

L

V

E

S

G

L

V

Q

P

G

S

R

K

L

S

C

A

S

25

26

G

F

T

F

S

D

Y

G

M

A

W

V

R

Q

A

P

G

K

G

P

E

W

V

A

F

50

51

I

S

N

L

A

Y

S

I

Y

A

D

T

V

T

G

R

F

T

I

S

R

E

N

A

75

76

K

N

T

L

Y

L

E

M

S

L

R

S

E

D

T

A

M

Y

C

A

R

Y

D

100

101

Y

D

N

I

L

D

Y

V

M

D

Y

W

G

Q

G

T

S

V

T

V

S

A

K

T

125

126

T

P

S

V

Y

P

L

A

P

G

C

G

D

T

G

S

V

T

L

G

C

L

150

151

V

K

G

Y

F

P

E

S

V

T

V

T

W

N

S

G

S

L

S

V

H

T

F

175

176

P

A

L

Q

S

G

L

Y

T

M

S

V

T

V

P

S

T

W

P

S

Q

200

201

T

V

T

C

S

V

A

H

P

A

S

T

V

D

K

L

E

P

S

G

P

I

225

226

S

T

I

N

P

C

231

Chain 3

1

E

F

R

H

D

S

G

Y

E

V

10

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

Charged residues and Proline are highlighed in blue.

Description

Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex with human Abeta-pE3-12PEGb

"They present three separate monoclonal antibodies that specifically recognize ABeta pE3 and inhibit ABeta pE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in ABeta pE3 oligomer-treated mice. Crystal structures of F ab -ABeta pE3 complexes revealed two distinct binding modes for the peptide. Juxtaposition of pyroglutamate pE3 and the F4 side chain (the ""pEF head"") confers a pronounced bulky hydrophobic nature to the ABeta pE3 N terminus that might explain the enhanced aggregation properties of the modified peptide. The deep burial of the pEF head by two of the antibodies explains their high target specificity and low cross-reactivity."

Literature

PMID:	28623233
Author(s):	Piechotta, A., Parthier, C., Kleinschmidt, M., Gnoth, K., Pillot, T., Lues, I., Demuth, H.U., Schilling, S., Rahfeld, J.U., Stubbs, M.T.
Reference:	J Biol Chem. 2017 Jul 28;292(30):12713-12724.

Download

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

Protein Information

Protein Name:	Amyloid-beta
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:	219 , 231 , 10
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5MY4
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 2-mer -A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.21
R free:	0.25

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
PCA	C	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

D

V

M

T

Q

T

P

L

S

L

P

V

S

L

G

D

Q

A

S

I

S

C

R

S

25

26

S

Q

S

L

V

H

S

D

G

N

T

Y

L

H

W

Y

L

Q

K

P

G

Q

S

P

K

50

51

L

I

Y

K

V

S

N

R

F

S

G

V

P

D

R

F

S

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

V

E

A

E

D

L

G

V

Y

F

C

S

Q

S

T

H

V

P

100

101

P

T

F

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 2

1

E

V

K

L

V

E

S

G

L

V

Q

P

G

S

R

K

L

S

C

A

S

25

26

G

F

T

F

S

D

Y

G

M

A

W

V

R

Q

A

P

G

K

G

P

E

W

V

A

F

50

51

I

S

N

L

A

Y

S

I

Y

A

D

T

V

T

G

R

F

T

I

S

R

E

N

A

75

76

K

N

T

L

Y

L

E

M

S

L

R

S

E

D

T

A

M

Y

C

A

R

Y

D

100

101

Y

D

N

I

L

D

Y

V

M

D

Y

W

G

Q

G

T

S

V

T

V

S

A

K

T

125

126

T

P

S

V

Y

P

L

A

P

G

C

G

D

T

G

S

V

T

L

G

C

L

150

151

V

K

G

Y

F

P

E

S

V

T

V

T

W

N

S

G

S

L

S

V

H

T

F

175

176

P

A

L

Q

S

G

L

Y

T

M

S

V

T

V

P

S

T

W

P

S

Q

200

201

T

V

T

C

S

V

A

H

P

A

S

T

V

D

K

L

E

P

S

G

P

I

225

226

S

T

I

N

P

C

231

Chain 3

1

E

F

G

H

D

S

G

F

E

V

R

H

Q

K

L

V

16

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

Charged residues and Proline are highlighed in blue.

Description

Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex with murine Abeta-pE3-18PEGb

"They present three separate monoclonal antibodies that specifically recognize ABeta pE3 and inhibit ABeta pE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in ABeta pE3 oligomer-treated mice. Crystal structures of F ab -ABeta pE3 complexes revealed two distinct binding modes for the peptide. Juxtaposition of pyroglutamate pE3 and the F4 side chain (the ""pEF head"") confers a pronounced bulky hydrophobic nature to the ABeta pE3 N terminus that might explain the enhanced aggregation properties of the modified peptide. The deep burial of the pEF head by two of the antibodies explains their high target specificity and low cross-reactivity."

Literature

PMID:	28623233
Author(s):	Piechotta, A., Parthier, C., Kleinschmidt, M., Gnoth, K., Pillot, T., Lues, I., Demuth, H.U., Schilling, S., Rahfeld, J.U., Stubbs, M.T.
Reference:	J Biol Chem. 2017 Jul 28;292(30):12713-12724.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:	ABPP, Alzheimer disease amyloid A4 protein homolog, Amyloid precursor protein, Amyloid-beta precursor protein, Amyloidogenic glycoprotein
Gene Name:	App
Sequence Length:	219 , 231 , 16
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5MYK
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 2-mer -A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.6
R free:	0.21

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
PCA	C	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

D

V

M

T

Q

T

P

L

T

L

S

V

T

I

G

Q

P

A

S

I

S

C

K

S

25

26

S

Q

S

L

Y

S

D

G

K

T

Y

L

N

W

L

Q

R

P

G

Q

S

P

M

50

51

R

L

I

Y

L

V

S

K

L

D

S

G

V

P

D

R

F

T

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

V

E

A

E

D

L

G

V

Y

C

V

Q

G

T

H

F

P

100

101

F

T

F

G

S

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 2

1

E

V

Q

L

Q

S

G

P

E

L

V

K

P

G

A

S

M

K

I

S

C

K

A

S

25

26

G

Y

S

F

T

G

Y

T

M

N

W

V

K

Q

S

H

G

K

N

L

E

W

I

G

L

50

51

I

N

P

Y

N

G

V

T

R

Y

N

Q

K

F

K

G

K

A

T

L

I

V

D

K

S

75

76

S

T

A

Y

M

E

L

S

L

T

S

E

D

S

A

V

Y

C

T

R

E

A

100

101

K

R

E

W

D

E

T

Y

W

G

Q

G

T

L

V

T

V

S

A

K

T

P

125

126

S

V

Y

P

L

A

P

G

S

A

Q

T

N

S

M

V

T

L

G

C

L

V

K

G

150

151

Y

F

P

E

P

V

T

V

T

W

N

S

G

S

L

S

G

V

H

T

F

P

A

V

175

176

L

Q

S

D

L

Y

T

L

S

V

T

V

P

S

T

W

P

S

E

T

V

T

200

201

C

N

V

A

H

P

A

S

T

K

V

D

K

I

V

P

R

D

C

G

C

K

P

225

226

C

I

C

228

Chain 3

1

D

V

M

T

Q

T

P

L

T

L

S

V

T

I

G

Q

P

A

S

I

S

C

K

S

25

26

S

Q

S

L

Y

S

D

G

K

T

Y

L

N

W

L

Q

R

P

G

Q

S

P

M

50

51

R

L

I

Y

L

V

S

K

L

D

S

G

V

P

D

R

F

T

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

V

E

A

E

D

L

G

V

Y

C

V

Q

G

T

H

F

P

100

101

F

T

F

G

S

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 4

1

E

V

Q

L

Q

S

G

P

E

L

V

K

P

G

A

S

M

K

I

S

C

K

A

S

25

26

G

Y

S

F

T

G

Y

T

M

N

W

V

K

Q

S

H

G

K

N

L

E

W

I

G

L

50

51

I

N

P

Y

N

G

V

T

R

Y

N

Q

K

F

K

G

K

A

T

L

I

V

D

K

S

75

76

S

T

A

Y

M

E

L

S

L

T

S

E

D

S

A

V

Y

C

T

R

E

A

100

101

K

R

E

W

D

E

T

Y

W

G

Q

G

T

L

V

T

V

S

A

K

T

P

125

126

S

V

Y

P

L

A

P

G

S

A

Q

T

N

S

M

V

T

L

G

C

L

V

K

G

150

151

Y

F

P

E

P

V

T

V

T

W

N

S

G

S

L

S

G

V

H

T

F

P

A

V

175

176

L

Q

S

D

L

Y

T

L

S

V

T

V

P

S

T

W

P

S

E

T

V

T

200

201

C

N

V

A

H

P

A

S

T

K

V

D

K

I

V

P

R

D

C

G

C

K

P

225

226

C

I

C

228

Chain 5

1

E

F

R

H

D

S

G

Y

E

V

10

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

Charged residues and Proline are highlighed in blue.

Description

Structure of Pyroglutamate-Abeta-specific Fab c#6 in complex with human Abeta-pE3-12-PEGb

"They present three separate monoclonal antibodies that specifically recognize ABeta pE3 and inhibit ABeta pE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in ABeta pE3 oligomer-treated mice. Crystal structures of F ab -ABeta pE3 complexes revealed two distinct binding modes for the peptide. Juxtaposition of pyroglutamate pE3 and the F4 side chain (the ""pEF head"") confers a pronounced bulky hydrophobic nature to the ABeta pE3 N terminus that might explain the enhanced aggregation properties of the modified peptide. The deep burial of the pEF head by two of the antibodies explains their high target specificity and low cross-reactivity."

Literature

PMID:	28623233
Author(s):	Piechotta, A., Parthier, C., Kleinschmidt, M., Gnoth, K., Pillot, T., Lues, I., Demuth, H.U., Schilling, S., Rahfeld, J.U., Stubbs, M.T.
Reference:	J Biol Chem. 2017 Jul 28;292(30):12713-12724.

Download

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

Protein Information

Protein Name:	Amyloid-beta
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:	219 , 228 , 219 , 228 , 10
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5MYO
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 2-mer -A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.59
R free:	0.215

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
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
GOL	C	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PCA	E	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

D

V

L

T

Q

T

P

L

T

L

S

V

T

I

G

Q

P

A

S

I

S

C

K

S

25

26

S

Q

S

L

Y

S

N

G

K

T

Y

L

N

W

L

Q

R

P

G

Q

S

P

K

50

51

R

L

I

Y

V

S

K

L

D

S

G

V

P

D

R

F

T

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

V

E

A

E

D

L

G

V

Y

C

V

Q

G

T

H

F

P

100

101

F

T

F

G

S

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 2

1

E

V

Q

L

Q

S

G

A

E

L

V

R

P

G

S

V

K

I

S

C

K

A

S

25

26

G

Y

I

F

N

Y

W

I

N

W

V

K

Q

R

P

G

Q

G

L

E

W

I

G

Q

50

51

I

Y

P

G

D

G

D

T

N

Y

N

G

K

F

K

G

K

A

T

L

T

A

D

K

S

75

76

S

T

A

Y

M

Q

L

S

L

T

S

E

D

S

A

V

Y

F

C

A

R

E

G

100

101

Y

I

V

Y

W

G

Q

G

T

L

V

T

V

S

A

K

T

P

S

V

Y

P

125

126

L

A

P

G

S

A

Q

T

N

S

M

V

T

L

G

C

L

V

K

G

Y

F

P

E

150

151

P

V

T

V

T

W

N

S

G

S

L

S

G

V

H

T

F

P

A

V

L

Q

S

D

175

176

L

Y

T

L

S

V

T

V

P

S

T

W

P

S

E

T

V

T

C

N

V

A

200

201

H

P

A

S

T

K

V

D

K

I

V

P

R

D

C

G

C

K

P

C

I

C

T

225

226

V

P

E

V

S

V

F

I

F

P

K

P

K

D

V

L

T

I

T

L

T

248

Chain 3

1

D

V

L

T

Q

T

P

L

T

L

S

V

T

I

G

Q

P

A

S

I

S

C

K

S

25

26

S

Q

S

L

Y

S

N

G

K

T

Y

L

N

W

L

Q

R

P

G

Q

S

P

K

50

51

R

L

I

Y

V

S

K

L

D

S

G

V

P

D

R

F

T

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

V

E

A

E

D

L

G

V

Y

C

V

Q

G

T

H

F

P

100

101

F

T

F

G

S

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 4

1

E

V

Q

L

Q

S

G

A

E

L

V

R

P

G

S

V

K

I

S

C

K

A

S

25

26

G

Y

I

F

N

Y

W

I

N

W

V

K

Q

R

P

G

Q

G

L

E

W

I

G

Q

50

51

I

Y

P

G

D

G

D

T

N

Y

N

G

K

F

K

G

K

A

T

L

T

A

D

K

S

75

76

S

T

A

Y

M

Q

L

S

L

T

S

E

D

S

A

V

Y

F

C

A

R

E

G

100

101

Y

I

V

Y

W

G

Q

G

T

L

V

T

V

S

A

K

T

P

S

V

Y

P

125

126

L

A

P

G

S

A

Q

T

N

S

M

V

T

L

G

C

L

V

K

G

Y

F

P

E

150

151

P

V

T

V

T

W

N

S

G

S

L

S

G

V

H

T

F

P

A

V

L

Q

S

D

175

176

L

Y

T

L

S

V

T

V

P

S

T

W

P

S

E

T

V

T

C

N

V

A

200

201

H

P

A

S

T

K

V

D

K

I

V

P

R

D

C

G

C

K

P

C

I

C

T

225

226

V

P

E

V

S

V

F

I

F

P

K

P

K

D

V

L

T

I

T

L

T

248

Chain 5

1

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

16

Chain 6

1

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

16

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

Charged residues and Proline are highlighed in blue.

Description

Structure of Pyroglutamate-Abeta-specific Fab c#24 in complex with human Abeta-pE3-18

"They present three separate monoclonal antibodies that specifically recognize ABeta pE3 and inhibit ABeta pE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in ABeta pE3 oligomer-treated mice. Crystal structures of F ab -ABeta pE3 complexes revealed two distinct binding modes for the peptide. Juxtaposition of pyroglutamate pE3 and the F4 side chain (the ""pEF head"") confers a pronounced bulky hydrophobic nature to the ABeta pE3 N terminus that might explain the enhanced aggregation properties of the modified peptide. The deep burial of the pEF head by two of the antibodies explains their high target specificity and low cross-reactivity."

Literature

PMID:	28623233
Author(s):	Piechotta, A., Parthier, C., Kleinschmidt, M., Gnoth, K., Pillot, T., Lues, I., Demuth, H.U., Schilling, S., Rahfeld, J.U., Stubbs, M.T.
Reference:	J Biol Chem. 2017 Jul 28;292(30):12713-12724.

Download

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

Protein Information

Protein Name:	Amyloid-beta
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:	219 , 248 , 219 , 248 , 16 , 16
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5MYX
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 2-mer -A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.49
R free:	0.213

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
PCA	B	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N
PCA	D	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N
PCA	E	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N
PCA	F	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

I

T

G

T

S

T

V

G

V

G

R

G

V

L

G

D

Q

K

N

I

N

T

Y

S

25

26

T

Y

L

Q

D

N

T

R

G

N

G

I

F

T

Y

D

A

K

Y

R

T

L

50

51

P

G

S

L

W

A

D

A

D

N

Q

F

A

S

Y

D

A

P

A

V

D

A

H

Y

75

76

Y

A

G

V

T

Y

D

Y

K

N

V

H

N

R

L

S

Y

D

G

N

A

I

100

101

R

S

V

H

Y

S

Q

G

Y

N

A

F

W

N

G

S

Q

M

V

Y

G

D

G

125

126

D

G

Q

T

F

I

P

L

S

G

I

D

V

A

H

E

L

T

H

A

V

T

D

150

151

Y

T

A

G

L

I

Y

Q

N

E

S

G

A

I

N

E

A

I

S

D

I

F

G

T

L

175

176

V

E

F

Y

A

N

K

N

P

D

W

E

I

G

E

D

V

Y

T

P

G

I

S

G

D

200

201

S

L

R

S

M

S

D

P

A

K

Y

G

D

P

D

H

Y

S

K

R

Y

T

G

T

Q

225

226

D

N

G

V

H

I

N

S

G

I

N

K

A

Y

L

I

S

Q

G

T

H

250

251

Y

G

V

S

V

G

I

G

R

D

K

L

G

K

I

F

Y

R

A

L

T

Q

Y

L

275

276

T

P

T

S

N

F

S

Q

L

R

A

V

Q

S

A

T

D

L

Y

G

S

T

S

300

301

Q

E

V

A

S

V

K

Q

A

F

D

A

V

G

V

K

316

Chain 2

1

G

A

I

G

5

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

Charged residues and Proline are highlighed in blue.

Description

Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd-substituted Thermolysin

The interaction of the amyloid-Beta peptide (ABeta) with thermolysin (TLN) was investigated by X-ray crystallography. Structural models of the complexes of TLN with several ABeta fragments show that, despite the numerous possible cleavage sites of the ABeta sequence, the C-terminal product of Ala30-Ile31 cleavage does not dissociate, thus inhibiting the enzyme. The high similarity between the TLN structural motif and neprilysin (NEP), the most extensively studied peptidase associated with ABeta clearance, suggests that NEP should be more efficient against ABeta polymorphs where Ala30-Ile31 is inaccessible.

Literature

PMID:	30403288
Author(s):	Leite, J.P., Gales, L.
Reference:	FEBS Lett. 2019 Jan;593(1):128-137.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:	Neutral protease & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:	nprS, nprM & APP, A4, AD1
Sequence Length:	316 , 5
Species:
Mutation(s):	No
E.C. Number:	3.4.24.27
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5ONP
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.34
R free:	0.18

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
CD	A	Cd 2	112.41	CADMIUM ION	[Cd+2]	WLZRMCYVCSSEQC-UHFFFAOYSA-N
DMS	A	C2 H6 O S	78.13	DIMETHYL SULFOXIDE	CS(=O)C	IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

I

T

G

T

S

T

V

G

V

G

R

G

V

L

G

D

Q

K

N

I

N

T

Y

S

25

26

T

Y

L

Q

D

N

T

R

G

N

G

I

F

T

Y

D

A

K

Y

R

T

L

50

51

P

G

S

L

W

A

D

A

D

N

Q

F

A

S

Y

D

A

P

A

V

D

A

H

Y

75

76

Y

A

G

V

T

Y

D

Y

K

N

V

H

N

R

L

S

Y

D

G

N

A

I

100

101

R

S

V

H

Y

S

Q

G

Y

N

A

F

W

N

G

S

Q

M

V

Y

G

D

G

125

126

D

G

Q

T

F

I

P

L

S

G

I

D

V

A

H

E

L

T

H

A

V

T

D

150

151

Y

T

A

G

L

I

Y

Q

N

E

S

G

A

I

N

E

A

I

S

D

I

F

G

T

L

175

176

V

E

F

Y

A

N

K

N

P

D

W

E

I

G

E

D

V

Y

T

P

G

I

S

G

D

200

201

S

L

R

S

M

S

D

P

A

K

Y

G

D

P

D

H

Y

S

K

R

Y

T

G

T

Q

225

226

D

N

G

V

H

I

N

S

G

I

N

K

A

Y

L

I

S

Q

G

T

H

250

251

Y

G

V

S

V

G

I

G

R

D

K

L

G

K

I

F

Y

R

A

L

T

Q

Y

L

275

276

T

P

T

S

N

F

S

Q

L

R

A

V

Q

S

A

T

D

L

Y

G

S

T

S

300

301

Q

E

V

A

S

V

K

Q

A

F

D

A

V

G

V

K

316

Chain 2

1

G

A

I

G

5

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

Charged residues and Proline are highlighed in blue.

Description

Alzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd-substituted Thermolysin

The interaction of the amyloid-Beta peptide (ABeta) with thermolysin (TLN) was investigated by X-ray crystallography. Structural models of the complexes of TLN with several ABeta fragments show that, despite the numerous possible cleavage sites of the ABeta sequence, the C-terminal product of Ala30-Ile31 cleavage does not dissociate, thus inhibiting the enzyme. The high similarity between the TLN structural motif and neprilysin (NEP), the most extensively studied peptidase associated with ABeta clearance, suggests that NEP should be more efficient against ABeta polymorphs where Ala30-Ile31 is inaccessible.

Literature

PMID:	30403288
Author(s):	Leite, J.P., Gales, L.
Reference:	FEBS Lett. 2019 Jan;593(1):128-137.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:	Neutral protease & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:	nprS, nprM & APP, A4, AD1
Sequence Length:	316 , 5
Species:
Mutation(s):	No
E.C. Number:	3.4.24.27
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5ONQ
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.17
R free:	0.172

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
CD	A	Cd 2	112.41	CADMIUM ION	[Cd+2]	WLZRMCYVCSSEQC-UHFFFAOYSA-N
DMS	A	C2 H6 O S	78.13	DIMETHYL SULFOXIDE	CS(=O)C	IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

I

T

G

T

S

T

V

G

V

G

R

G

V

L

G

D

Q

K

N

I

N

T

Y

S

25

26

T

Y

L

Q

D

N

T

R

G

N

G

I

F

T

Y

D

A

K

Y

R

T

L

50

51

P

G

S

L

W

A

D

A

D

N

Q

F

A

S

Y

D

A

P

A

V

D

A

H

Y

75

76

Y

A

G

V

T

Y

D

Y

K

N

V

H

N

R

L

S

Y

D

G

N

A

I

100

101

R

S

V

H

Y

S

Q

G

Y

N

A

F

W

N

G

S

Q

M

V

Y

G

D

G

125

126

D

G

Q

T

F

I

P

L

S

G

I

D

V

A

H

E

L

T

H

A

V

T

D

150

151

Y

T

A

G

L

I

Y

Q

N

E

S

G

A

I

N

E

A

I

S

D

I

F

G

T

L

175

176

V

E

F

Y

A

N

K

N

P

D

W

E

I

G

E

D

V

Y

T

P

G

I

S

G

D

200

201

S

L

R

S

M

S

D

P

A

K

Y

G

D

P

D

H

Y

S

K

R

Y

T

G

T

Q

225

226

D

N

G

V

H

I

N

S

G

I

N

K

A

Y

L

I

S

Q

G

T

H

250

251

Y

G

V

S

V

G

I

G

R

D

K

L

G

K

I

F

Y

R

A

L

T

Q

Y

L

275

276

T

P

T

S

N

F

S

Q

L

R

A

V

Q

S

A

T

D

L

Y

G

S

T

S

300

301

Q

E

V

A

S

V

K

Q

A

F

D

A

V

G

V

K

316

Chain 2

1

I

G

3

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

Charged residues and Proline are highlighed in blue.

Description

Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin

The interaction of the amyloid-Beta peptide (ABeta) with thermolysin (TLN) was investigated by X-ray crystallography. Structural models of the complexes of TLN with several ABeta fragments show that, despite the numerous possible cleavage sites of the ABeta sequence, the C-terminal product of Ala30-Ile31 cleavage does not dissociate, thus inhibiting the enzyme. The high similarity between the TLN structural motif and neprilysin (NEP), the most extensively studied peptidase associated with ABeta clearance, suggests that NEP should be more efficient against ABeta polymorphs where Ala30-Ile31 is inaccessible.

Literature

PMID:	30403288
Author(s):	Leite, J.P., Gales, L.
Reference:	FEBS Lett. 2019 Jan;593(1):128-137.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:	Thermostable neutral proteinase & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:	npr & APP, A4, AD1
Sequence Length:	316 , 3
Species:
Mutation(s):	No
E.C. Number:	3.4.24.27
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5ONR
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.39
R free:	0.19899999

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
DMS	A	C2 H6 O S	78.13	DIMETHYL SULFOXIDE	CS(=O)C	IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	A	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N

Structure

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

Sequence & Sec. Str.

Chain 1

1

Q

S

V

L

T

Q

P

S

V

S

A

P

G

Q

T

V

T

I

S

C

S

G

S

25

26

S

N

I

G

N

Y

V

S

W

Y

Q

H

L

P

G

T

A

P

K

F

L

I

Y

50

51

D

N

K

R

P

S

G

I

P

D

R

F

S

G

F

K

S

G

T

S

A

T

L

G

75

76

I

T

G

L

Q

T

G

D

E

A

D

Y

C

G

T

W

D

S

L

S

A

L

V

100

101

F

G

T

K

L

T

V

L

110

Chain 2

1

Q

S

V

L

T

Q

P

S

V

S

A

P

G

Q

T

V

T

I

S

C

S

G

S

25

26

S

N

I

G

N

Y

V

S

W

Y

Q

H

L

P

G

T

A

P

K

F

L

I

Y

50

51

D

N

K

R

P

S

G

I

P

D

R

F

S

G

F

K

S

G

T

S

A

T

L

G

75

76

I

T

G

L

Q

T

G

D

E

A

D

Y

C

G

T

W

D

S

L

S

A

L

V

100

101

F

G

T

K

L

T

V

L

110

Chain 3

1

Q

S

V

L

T

Q

P

S

V

S

A

P

G

Q

T

V

T

I

S

C

S

G

S

25

26

S

N

I

G

N

Y

V

S

W

Y

Q

H

L

P

G

T

A

P

K

F

L

I

Y

50

51

D

N

K

R

P

S

G

I

P

D

R

F

S

G

F

K

S

G

T

S

A

T

L

G

75

76

I

T

G

L

Q

T

G

D

E

A

D

Y

C

G

T

W

D

S

L

S

A

L

V

100

101

F

G

T

K

L

T

V

L

110

Chain 4

1

Q

S

V

L

T

Q

P

S

V

S

A

P

G

Q

T

V

T

I

S

C

S

G

S

25

26

S

N

I

G

N

Y

V

S

W

Y

Q

H

L

P

G

T

A

P

K

F

L

I

Y

50

51

D

N

K

R

P

S

G

I

P

D

R

F

S

G

F

K

S

G

T

S

A

T

L

G

75

76

I

T

G

L

Q

T

G

D

E

A

D

Y

C

G

T

W

D

S

L

S

A

L

V

100

101

F

G

T

K

L

T

V

L

110

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

Charged residues and Proline are highlighed in blue.

Description

Immunoglobulin light chain variable domain AL-T05

They present the crystal structure of Lambda1 AL-T05 with an altered dimer rotated 180Â° from the canonical dimer. It shows fast aggregation kinetics.

Literature

PMID:	28074646
Author(s):	Blancas-Mejia, L.M., Misra, P., Ramirez-Alvarado, M.
Reference:	Biochemistry. 2017 Feb 7;56(5):757-766.

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

Protein Information

Protein Name:	Immunoglobulin light chain variable domain AL-T05
Alternative Name:
Gene Name:
Sequence Length:	110
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient

Structure Information

PDB ID:	5T93
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:	0.223

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

Structure

Press 'p' to pause
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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

N

K

G

A

I

F

6

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

Charged residues and Proline are highlighed in blue.

Description

Structure of amyloid-beta derived peptide - NKGAIF

They characterize two segments of the protein amyloid Beta (ABeta) known to form fibrils in Alzheimer's disease patients. We designed two variants of ABeta(19-24) and ABeta(27-32), IFAEDV (I6V) and NKGAIF (N6F) to lower the aggregation propensity of individual peptides while maintaining the similar interactions between the two segments in their native forms. They found that the variants do not form significant amyloid fibrils individually but a 1:1 mixture forms abundant fibrils. Hetero-oligomers up to decamers were found in the mixture while the individual peptides formed primarily dimers and some tetramers consistent with a strong heterotypic interaction between the two segments.

Literature

PMID:	29349888
Author(s):	Do, T.D., Sangwan, S., de Almeida, N.E.C., Ilitchev, A.I., Giammona, M., Sawaya, M.R., Buratto, S.K., Eisenberg, D.S., Bowers, M.T.
Reference:	Protein Sci. 2018 Jul;27(7):1181-1190.

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

Protein Information

Protein Name:	Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:	6
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P05067
Keyword(s):	Amyloid beta A4 protein

Structure Information

PDB ID:	5TXD
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 8-mer - A8
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.45
R free:	0.191

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
PO4	Z	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

I

F

A

E

D

V

6

Chain 2

1

I

F

A

E

D

V

6

Chain 3

1

I

F

A

E

D

V

6

Chain 4

1

I

F

A

E

D

V

6

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

Charged residues and Proline are highlighed in blue.

Description

Polymorphic form 2 of amyloid-beta derived peptide - IFAEDV

They characterize two segments of the protein amyloid Beta (ABeta) known to form fibrils in Alzheimer's disease patients. We designed two variants of ABeta(19-24) and ABeta(27-32), IFAEDV (I6V) and NKGAIF (N6F) to lower the aggregation propensity of individual peptides while maintaining the similar interactions between the two segments in their native forms. They found that the variants do not form significant amyloid fibrils individually but a 1:1 mixture forms abundant fibrils. Hetero-oligomers up to decamers were found in the mixture while the individual peptides formed primarily dimers and some tetramers consistent with a strong heterotypic interaction between the two segments.

Literature

PMID:	29349888
Author(s):	Do, T.D., Sangwan, S., de Almeida, N.E.C., Ilitchev, A.I., Giammona, M., Sawaya, M.R., Buratto, S.K., Eisenberg, D.S., Bowers, M.T.
Reference:	Protein Sci. 2018 Jul;27(7):1181-1190.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:	6
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	IFAEDV

Structure Information

PDB ID:	5TXH
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 8-mer - A8
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.45
R free:	0.138

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
IPA	D	C3 H8 O	60.1	ISOPROPYL ALCOHOL	CC(C)O	KFZMGEQAYNKOFK-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network

Sequence & Sec. Str.

Chain 1

1

I

H

V

H

L

Q

I

7

Chain 2

1

I

H

V

H

L

Q

I

7

Chain 3

1

I

H

V

H

L

Q

I

7

Chain 4

1

I

H

V

H

L

Q

I

7

Chain 5

1

I

H

V

H

L

Q

I

7

Chain 6

1

I

H

V

H

L

Q

I

7

Chain 7

1

I

H

V

H

L

Q

I

7

Chain 8

1

I

H

V

H

L

Q

I

7

Chain 9

1

I

H

V

H

L

Q

I

7

Chain 10

1

I

H

V

H

L

Q

I

7

Chain 11

1

I

H

V

H

L

Q

I

7

Chain 12

1

I

H

V

H

L

Q

I

7

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

Charged residues and Proline are highlighed in blue.

Description

Zinc-Binding Structure of a Catalytic Amyloid from Solid-State NMR Spectroscopy

They determine the structure of a zinc-bound metalloamyloid that catalyzes ester hydrolysis. The peptide forms amphiphilic parallel Beta-sheets that assemble into stacked bilayers with alternating hydrophobic and polar interfaces. The hydrophobic interface is stabilized by apolar side chains from adjacent sheets, whereas the hydrated polar interface houses the Zn 2+ -binding histidines with binding geometries unusual in proteins. Each Zn 2+ has two bis-coordinated histidine ligands, which bridge adjacent strands to form an infinite metal-ligand chain along the fibril axis. A third histidine completes the protein ligand environment, leaving a free site on the Zn 2+ for water activation.

Literature

PMID:	28566494
Author(s):	Lee, M., Wang, T., Makhlynets, O.V., Wu, Y., Polizzi, N.F., Wu, H., Gosavi, P.M., Stohr, J., Korendovych, I.V., DeGrado, W.F., Hong, M.
Reference:	Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6191-6196.

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

Protein Information

Protein Name:	Synthetic
Alternative Name:
Gene Name:
Sequence Length:	7
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ILE-HIS-VAL-HIS-LEU-GLN-ILE

Structure Information

PDB ID:	5UGK
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 12-mer - A12
PDB Classification:	METAL BINDING PROTEIN
Method:	SOLID-STATE NMR
Resolution (Å):
R free:

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
ZN	A	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	C	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	E	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	I	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	K	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	O	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	Q	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	S	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	U	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	W	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
ZN	Y	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

R

L

A

N

F

L

V

A

I

K

X

K

X

14

Chain 2

1

A

R

L

A

N

F

L

V

A

I

K

X

K

X

14

Chain 3

1

A

R

L

A

N

F

L

V

A

I

K

X

K

X

14

Chain 4

1

A

R

L

A

N

F

L

V

A

I

K

X

K

X

14

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

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of (Cit)LANFLV heptapeptide segment from islet amyloid polypeptide (IAPP) incorporated into a macrocyclic beta-sheet template

Peptides derived from residues 11-17 of IAPP that assemble to form tetramers. Incorporation of residues 11-17 of IAPP (RLANFLV) into a macrocyclic Beta-sheet peptide results in a monomeric peptide that does not self-assemble to form oligomers. The tetramers consist of hydrogen-bonded dimers that sandwich together through hydrophobic interactions. The tetramers share several features with structures reported for IAPP fibrils and demonstrate the importance of hydrogen bonding and hydrophobic interactions in the oligomerization of IAPP-derived peptides.

Literature

PMID:	28661686
Author(s):	Wang, Y., Kreutzer, A.G., Truex, N.L., Nowick, J.S.
Reference:	J Org Chem. 2017 Aug 4;82(15):7905-7912.

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

Protein Information

Protein Name:	Islet amyloid polypeptide (IAPP)
Alternative Name:
Gene Name:
Sequence Length:	14
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-CIR-LEU-ALA-ASN-PHE-LEU-VAL-ORN-ILE-LYS-HAO-LYS-A8E

Structure Information

PDB ID:	5UHR
Amyloid Category:	Non-amyloid
Type:	Fibril
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.8
R free:	0.264

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
A8E	A	C5 H8 Br N O2	194.03	(2S)-2-amino-4-bromopent-4-enoic acid	C=C(C[C@@H](C(=O)O)N)Br	YTCSGBSYHNQHFD-BYPYZUCNSA-N
CIR	A	C6 H13 N3 O3	175.19	CITRULLINE	C(C[C@@H](C(=O)O)N)CNC(=O)N	RHGKLRLOHDJJDR-BYPYZUCNSA-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
A8E	B	C5 H8 Br N O2	194.03	(2S)-2-amino-4-bromopent-4-enoic acid	C=C(C[C@@H](C(=O)O)N)Br	YTCSGBSYHNQHFD-BYPYZUCNSA-N
CIR	B	C6 H13 N3 O3	175.19	CITRULLINE	C(C[C@@H](C(=O)O)N)CNC(=O)N	RHGKLRLOHDJJDR-BYPYZUCNSA-N
CL	B	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
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
A8E	C	C5 H8 Br N O2	194.03	(2S)-2-amino-4-bromopent-4-enoic acid	C=C(C[C@@H](C(=O)O)N)Br	YTCSGBSYHNQHFD-BYPYZUCNSA-N
CIR	C	C6 H13 N3 O3	175.19	CITRULLINE	C(C[C@@H](C(=O)O)N)CNC(=O)N	RHGKLRLOHDJJDR-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
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
A8E	D	C5 H8 Br N O2	194.03	(2S)-2-amino-4-bromopent-4-enoic acid	C=C(C[C@@H](C(=O)O)N)Br	YTCSGBSYHNQHFD-BYPYZUCNSA-N
CIR	D	C6 H13 N3 O3	175.19	CITRULLINE	C(C[C@@H](C(=O)O)N)CNC(=O)N	RHGKLRLOHDJJDR-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

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

K

L

V

F

A

E

A

I

G

L

M

V

17

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

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of macrocycles containing Abeta 16-22 (KLV(PHI)FAE) and Abeta 30-36 (AII(SAR)L(ORN)V)

The effect of shifting the residue pairing of the Beta-hairpins on the structures of the oligomers that form is explored through X-ray crystallography. Three residue pairings were investigated using constrained macrocyclic Beta-hairpins in which ABeta 30-36 is juxtaposed with ABeta 17-23 , ABeta 16-22 , and ABeta 15-21 . The ABeta 16-22 -ABeta 30-36 pairing forms a compact ball-shaped dodecamer composed of fused triangular trimers. This dodecamer may help explain the structures of the trimers and dodecamers formed by full-length ABeta.

Literature

PMID:	28683555
Author(s):	Salveson, P.J., Spencer, R.K., Kreutzer, A.G., Nowick, J.S.
Reference:	Org Lett. 2017 Jul 7;19(13):3462-3465.

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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:	17
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL

Structure Information

PDB ID:	5V63
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.0909999999999997
R free:	0.26899999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	A	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Q

K

L

V

F

A

I

G

L

M

V

16

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

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of macrocycles containing Abeta 15-21 (QKLV(PHI)FA) and Abeta 30-36 (AII(SAR)L(ORN)V)

The effect of shifting the residue pairing of the Beta-hairpins on the structures of the oligomers that form is explored through X-ray crystallography. Three residue pairings were investigated using constrained macrocyclic Beta-hairpins in which ABeta 30-36 is juxtaposed with ABeta 17-23 , ABeta 16-22 , and ABeta 15-21 . The ABeta 16-22 -ABeta 30-36 pairing forms a compact ball-shaped dodecamer composed of fused triangular trimers. This dodecamer may help explain the structures of the trimers and dodecamers formed by full-length ABeta.

Literature

PMID:	28683555
Author(s):	Salveson, P.J., Spencer, R.K., Kreutzer, A.G., Nowick, J.S.
Reference:	Org Lett. 2017 Jul 7;19(13):3462-3465.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-GLN-LYS-LEU-VAL-PHI-PHE-ALA-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL

Structure Information

PDB ID:	5V64
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.02
R free:	0.244

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
FLC	A	C6 H5 O7 -3	189.1	CITRATE ANION	C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O	KRKNYBCHXYNGOX-UHFFFAOYSA-K
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	A	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 2

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 3

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 4

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 5

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 6

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 7

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 8

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 9

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 10

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 11

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 12

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 13

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 14

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 15

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

Chain 16

1

A

L

V

F

A

E

D

A

I

G

L

M

V

16

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

Charged residues and Proline are highlighed in blue.

Description

X-ray Crystallographic Structure of a Compact Dodecamer from a Peptide Derived from A beta 16-36.

The effect of shifting the residue pairing of the Beta-hairpins on the structures of the oligomers that form is explored through X-ray crystallography. Three residue pairings were investigated using constrained macrocyclic Beta-hairpins in which ABeta 30-36 is juxtaposed with ABeta 17-23 , ABeta 16-22 , and ABeta 15-21 . The ABeta 16-22 -ABeta 30-36 pairing forms a compact ball-shaped dodecamer composed of fused triangular trimers. This dodecamer may help explain the structures of the trimers and dodecamers formed by full-length ABeta.

Literature

PMID:	28683555
Author(s):	Salveson, P.J., Spencer, R.K., Kreutzer, A.G., Nowick, J.S.
Reference:	Org Lett. 2017 Jul 7;19(13):3462-3465.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL

Structure Information

PDB ID:	5V65
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.52
R free:	0.281

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	A	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	B	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	C	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	D	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	E	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	F	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	G	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	G	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	G	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	H	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	H	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	H	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	I	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	I	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	I	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	J	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	J	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	J	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	K	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	K	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	K	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	L	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	L	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	L	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	M	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	M	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	M	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	N	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	N	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	N	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	O	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	O	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	O	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N
ORN	P	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	P	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SAR	P	C3 H7 N O2	89.09	SARCOSINE	CNCC(=O)O	FSYKKLYZXJSNPZ-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

K

L

V

F

A

E

A

E

A

F

V

L

K

16

Chain 2

1

A

K

L

V

F

A

E

A

E

A

F

V

L

K

16

Chain 3

1

A

K

L

V

F

A

E

A

E

A

F

V

L

K

16

Chain 4

1

A

K

L

V

F

A

E

A

E

A

F

V

L

K

16

Chain 5

1

A

K

L

V

F

A

E

A

E

A

F

V

L

K

16

Chain 6

1

A

K

L

V

F

A

E

A

E

A

F

V

L

K

16

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

Charged residues and Proline are highlighed in blue.

Description

X-ray Crystallographic Structure of a Giant Double-Walled Peptide Nanotube Formed by a Macrocyclic beta-Sheet Containing A beta 16-22.

The supramolecular assembly of a macrocyclic Beta-sheet containing residues 16-22 of the Beta-amyloid peptide, ABeta. X-ray crystallography reveals that the macrocyclic Beta-sheet assembles to form double-walled nanotubes, with an inner diameter of 7 nm and outer diameter of 11 nm. The inner wall is composed of an extended network of hydrogen-bonded dimers. The outer wall is composed of a separate extended network of Beta-barrel-like tetramers. These large peptide nanotubes pack into a hexagonal lattice that resembles a honeycomb.

Literature

PMID:	28598147
Author(s):	Chen, K.H., Corro, K.A., Le, S.P., Nowick, J.S.
Reference:	J Am Chem Soc. 2017 Jun 21;139(24):8102-8105.

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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:	16
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-GLU-ALA-PHE-MEA-VAL-LEU-LYS

Structure Information

PDB ID:	5VF1
Amyloid Category:	Non-amyloid
Type:	Fibril
Global Stoichiometry:	Homo 144-mer - A144
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.1
R free:	0.273

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MEA	A	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MEA	B	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MEA	C	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MEA	D	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MEA	E	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MEA	F	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

E

V

Q

L

Q

S

G

P

E

L

M

K

P

G

A

S

V

K

I

S

C

K

A

T

25

26

G

Y

T

F

S

T

S

W

I

E

W

I

K

Q

R

P

G

H

G

L

E

W

I

G

E

50

51

V

L

P

G

S

G

K

S

N

H

N

A

N

F

K

G

R

A

T

F

T

A

D

T

A

75

76

S

N

T

A

Y

M

Q

L

S

L

T

S

E

D

S

A

V

Y

C

A

R

E

G

100

101

S

N

A

L

A

Y

W

G

Q

G

T

L

V

T

V

S

A

S

T

K

G

P

125

126

S

V

F

P

L

A

P

S

K

S

T

S

G

T

A

L

G

C

L

V

K

D

150

151

Y

F

P

E

P

V

T

V

S

W

N

S

G

A

L

T

S

G

V

H

T

F

P

A

V

175

176

L

Q

S

G

L

Y

S

L

S

V

T

V

P

S

L

G

T

Q

T

Y

200

201

I

C

N

V

N

H

K

P

S

N

T

K

V

D

K

V

E

P

K

S

C

222

Chain 2

1

E

I

V

L

T

Q

S

P

A

I

M

S

A

S

P

G

E

K

V

T

M

T

C

S

A

25

26

S

V

S

Y

M

H

W

Y

Q

K

S

G

T

S

P

K

R

W

I

Y

D

S

50

51

S

R

L

A

S

G

V

P

S

R

F

S

G

S

G

T

S

Y

S

L

T

I

S

75

76

N

M

E

A

E

D

A

T

Y

F

C

Q

N

W

R

S

P

T

F

G

A

G

T

100

101

K

L

E

L

K

R

T

V

A

P

S

V

F

I

F

P

S

D

E

Q

L

K

S

125

126

G

T

A

S

V

C

L

N

F

Y

P

R

E

A

K

V

Q

W

K

V

D

N

150

151

A

L

Q

S

G

N

S

Q

E

S

V

T

E

Q

D

S

K

D

S

T

Y

S

L

S

175

176

T

L

T

L

S

K

A

D

Y

E

K

H

K

V

Y

A

C

E

V

T

H

Q

G

L

S

200

201

S

P

V

T

K

S

F

N

R

G

E

C

212

Chain 3

1

X

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

X

18

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

Charged residues and Proline are highlighed in blue.

Description

ANTIBODY C706 IN COMPLEX WTH BETA-AMYLOID PEPTIDE 1-16

Antibodies targeting the immunodominant N-terminal epitope of ABeta and capable of binding both the plaques and soluble species have been most efficacious in animal models. Structural studies of such antibodies with bound ABeta peptides provided the basis for understanding the mechanisms of action and the differences in potency. They determined the crystal structure of murine antibody C706 in complex with the N-terminal ABeta 1-16 peptide sequence.

Literature

PMID:	28830506
Author(s):	Teplyakov, A., Obmolova, G., Gilliland, G.L.
Reference:	Alzheimers Res Ther. 2017 Aug 22;9(1):66.

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

Protein Information

Protein Name:	Amyloid-beta
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:	222 , 212 , 18
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	5W3P
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 2-mer -A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.92
R free:	0.23600000

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
GOL	H	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PCA	H	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N
SO4	H	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	L	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
PCA	L	C5 H7 N O3	129.11	PYROGLUTAMIC ACID	C1CC(=O)N[C@@H]1C(=O)O	ODHCTXKNWHHXJC-VKHMYHEASA-N
SO4	L	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
ACE	P	C2 H4 O	44.05	ACETYL GROUP	CC=O	IKHGUXGNUITLKF-UHFFFAOYSA-N
NH2	P	H2 N	16.02	AMINO GROUP	[NH2]	QGZKDVFQNNGYKY-UHFFFAOYAF
SO4	P	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

K

L

V

F

A

E

A

I

G

L

M

V

16

Chain 2

1

A

K

L

V

F

A

E

A

I

G

L

M

V

16

Chain 3

1

A

K

L

V

F

A

E

A

I

G

L

M

V

16

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

Charged residues and Proline are highlighed in blue.

Description

X-ray crystallographic structure of a beta-hairpin peptide mimic derived from Abeta 16-36. Synchrotron data set. (ORN)KLV(MEA)FAE(ORN)AIIGLMV.

[ABeta oligomer] The peptide assembles to form a hexamer in the crystal state and that the hexamer is composed of dimers and trimers. Lactate dehydrogenase release assays show that the oligomers formed by the ABeta 16-36 Beta-hairpin peptide are toxic toward neuronally derived SH-SY5Y cells.

Literature

PMID:	29028351
Author(s):	Kreutzer, A.G., Spencer, R.K., McKnelly, K.J., Yoo, S., Hamza, I.L., Salveson, P.J., Nowick, J.S.
Reference:	Biochemistry. 2017 Nov 14;56(45):6061-6071.

Download

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

Protein Information

Protein Name:	Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL

Structure Information

PDB ID:	5W4H
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.72
R free:	0.237

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MEA	A	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA	B	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA	C	C10 H13 N O2	179.22	N-METHYLPHENYLALANINE	CN[C@@H](Cc1ccccc1)C(=O)O	SCIFESDRCALIIM-VIFPVBQESA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N

Structure database of aggregation related proteins and peptides

Displaying 451 to 480 records out of 565 records fetched.