SMTL ID : 8x7p.1

CCA-bound E46K alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

8 x V79: copper;trisodium;18-(2-carboxylatoethyl)-20-(carboxylatomethyl)-12-ethenyl-7-ethyl-3,8,13,17-tetramethyl-17,18-dihydroporphyrin-21,23-diide-2-carboxylate

V79.1: 8 residues within 4Å: Chain A: H.50, V.66 Chain E: H.50, G.51, V.66 Chain J: K.97 Ligands: V79.2, V79.5 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 2 interactions with chain J, Hydrophobic interactions: A:V.66 Salt bridges: E:K.97, J:K.97, J:K.97 V79.2: 7 residues within 4Å: Chain A: H.50, G.51, V.66 Chain B: H.50, V.66 Chain E: K.97 Ligands: V79.1 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 1 interactions with chain B, Salt bridges: E:K.97, E:K.97, A:K.97 Hydrophobic interactions: B:V.66 V79.3: 8 residues within 4Å: Chain C: H.50, V.66 Chain F: K.97 Chain G: H.50, G.51, V.66 Ligands: V79.4, V79.6 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F, 1 interactions with chain G, Hydrophobic interactions: C:V.66 Salt bridges: F:K.97, F:K.97, G:K.97 V79.4: 7 residues within 4Å: Chain C: H.50, G.51, V.66 Chain D: H.50, V.66 Chain G: K.97 Ligands: V79.3 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain G, Salt bridges: C:K.97, G:K.97, G:K.97 Hydrophobic interactions: D:V.66 V79.5: 8 residues within 4Å: Chain E: H.50, V.66 Chain I: K.97 Chain J: H.50, G.51, V.66 Ligands: V79.1, V79.8 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain I, 1 interactions with chain J, Hydrophobic interactions: E:V.66 Salt bridges: I:K.97, I:K.97, J:K.97 V79.6: 8 residues within 4Å: Chain F: H.50, G.51, V.66 Chain G: H.50, V.66 Chain H: K.97 Ligands: V79.3, V79.7 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H, Hydrophobic interactions: G:V.66 Salt bridges: H:K.97, H:K.97 V79.7: 5 residues within 4Å: Chain F: V.66 Chain H: H.50, G.51, V.66 Ligands: V79.6 1 PLIP interactions: 1 interactions with chain F, Hydrophobic interactions: F:V.66 V79.8: 5 residues within 4Å: Chain I: H.50, G.51, V.66 Chain J: V.66 Ligands: V79.5 1 PLIP interactions: 1 interactions with chain J, Hydrophobic interactions: J:V.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, K. et al., Binding adaptability of chemical ligands to polymorphic alpha-synuclein amyloid fibrils. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-09-11

Peptides

Alpha-synuclein: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Alpha-synuclein

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