SMTL ID : 7ynl.1

EB-bound alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

16 x IZ8: 4-azanyl-6-[[4-[4-[(~{E})-(8-azanyl-1-oxidanyl-5,7-disulfo-naphthalen-2-yl)diazenyl]-3-methyl-phenyl]-2-methyl-phenyl]diazenyl]-5-oxidanyl-naphthalene-1,3-disulfonic acid(Non-covalent)

IZ8.1: 8 residues within 4Å: Chain A: K.97 Chain C: Q.62 Chain D: K.97 Ligands: IZ8.4, IZ8.7, IZ8.9, IZ8.15, IZ8.16 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Salt bridges: A:K.97, D:K.97 IZ8.2: 9 residues within 4Å: Chain A: K.43, K.45 Chain D: K.43 Chain F: T.59 Ligands: IZ8.5, IZ8.8, IZ8.12, IZ8.13, IZ8.14 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 interactions with chain F Salt bridges: A:K.43, A:K.45, D:K.43 Hydrogen bonds: F:T.59, F:T.59 IZ8.3: 5 residues within 4Å: Chain A: Q.62 Chain B: K.97 Ligands: IZ8.4, IZ8.9, IZ8.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.97 IZ8.4: 7 residues within 4Å: Chain A: K.97 Chain B: K.97 Chain D: Q.62 Ligands: IZ8.1, IZ8.3, IZ8.9, IZ8.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.97, B:K.97 IZ8.5: 6 residues within 4Å: Chain A: K.43 Chain B: K.43, K.45 Ligands: IZ8.2, IZ8.13, IZ8.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.43, B:K.45, A:K.43 IZ8.6: 6 residues within 4Å: Chain C: K.43, K.45 Chain H: T.59 Ligands: IZ8.8, IZ8.10, IZ8.12 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:T.59, H:T.59 Salt bridges: C:K.43, C:K.45 IZ8.7: 5 residues within 4Å: Chain C: K.97 Chain D: K.97 Ligands: IZ8.1, IZ8.15, IZ8.16 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.97, D:K.97 IZ8.8: 8 residues within 4Å: Chain C: K.43 Chain D: K.43, K.45 Chain E: T.59 Ligands: IZ8.2, IZ8.6, IZ8.10, IZ8.12 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, 1 interactions with chain C Salt bridges: D:K.43, D:K.45, C:K.43 Hydrophobic interactions: E:T.59 IZ8.9: 9 residues within 4Å: Chain A: T.59 Chain E: K.43, K.45 Chain H: K.43 Ligands: IZ8.1, IZ8.3, IZ8.4, IZ8.11, IZ8.16 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, 1 interactions with chain H Salt bridges: E:K.43, E:K.45, H:K.43 Hydrogen bonds: A:T.59, A:T.59 IZ8.10: 6 residues within 4Å: Chain E: K.97 Chain G: Q.62 Chain H: K.97 Ligands: IZ8.6, IZ8.8, IZ8.12 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Salt bridges: H:K.97, E:K.97 IZ8.11: 7 residues within 4Å: Chain B: T.59 Chain E: K.43 Chain F: K.43, K.45 Ligands: IZ8.3, IZ8.4, IZ8.9 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B, 1 interactions with chain E Salt bridges: F:K.43, F:K.45, E:K.43 Hydrophobic interactions: B:T.59 IZ8.12: 8 residues within 4Å: Chain E: K.97 Chain F: K.97 Chain H: Q.62 Ligands: IZ8.2, IZ8.6, IZ8.8, IZ8.10, IZ8.14 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Salt bridges: F:K.97, E:K.97 IZ8.13: 4 residues within 4Å: Chain F: Q.62 Ligands: IZ8.2, IZ8.5, IZ8.14 No protein-ligand interaction detected (PLIP) IZ8.14: 6 residues within 4Å: Chain E: Q.62 Chain F: K.97 Ligands: IZ8.2, IZ8.5, IZ8.12, IZ8.13 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:K.97 IZ8.15: 6 residues within 4Å: Chain C: T.59 Chain G: K.43, K.45 Ligands: IZ8.1, IZ8.7, IZ8.16 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:T.59, C:T.59 Salt bridges: G:K.43, G:K.45 IZ8.16: 8 residues within 4Å: Chain D: T.59 Chain G: K.43 Chain H: K.43, K.45 Ligands: IZ8.1, IZ8.7, IZ8.9, IZ8.15 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D, 2 interactions with chain H Salt bridges: G:K.43, H:K.43, H:K.45 Hydrophobic interactions: D:T.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tao, Y.Q. et al., EB-bound alpha-synuclein fibrils. To Be Published

Release Date

2023-08-02

Peptides

Alpha-synuclein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
A

E
H

F
B

G
C

H
D

Alpha-synuclein

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