SMTL ID : 8x7l.1

EB-bound E46K alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

6 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

IZ8.1: 5 residues within 4Å: Chain E: K.58, K.60 Chain F: K.58, K.60 Ligands: IZ8.3 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Salt bridges: E:K.58, E:K.60, F:K.60 IZ8.2: 3 residues within 4Å: Chain G: K.58, K.60 Ligands: IZ8.3 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:K.58, G:K.60 IZ8.3: 6 residues within 4Å: Chain E: K.58, K.60 Chain G: K.58, K.60 Ligands: IZ8.1, IZ8.2 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain E Salt bridges: G:K.58, G:K.60, E:K.58, E:K.60 IZ8.4: 1 residues within 4Å: Ligands: IZ8.5 No protein-ligand interaction detected (PLIP) IZ8.5: 4 residues within 4Å: Chain H: K.58, K.60 Ligands: IZ8.4, IZ8.6 2 PLIP interactions: 2 interactions with chain H Salt bridges: H:K.58, H:K.60 IZ8.6: 5 residues within 4Å: Chain H: K.58, K.60 Chain I: K.58, K.60 Ligands: IZ8.5 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:K.58 Salt bridges: I:K.60, H:K.58, H:K.60

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
C

C
D

D
E

E
F

F
G

G
H

H
I

I
J

J
B

Alpha-synuclein

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