SMTL ID : 8xwd.1

Croy-EM structure of alpha synuclein fibril with EGCG

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x KDH: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate(Non-covalent)

KDH.1: 8 residues within 4Å: Chain A: L.38, K.80, V.82, E.83 Chain C: Y.39, E.46 Ligands: KDH.3, KDH.5 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Y.39, C:Y.39, C:E.46, A:K.80, A:E.83, A:E.83 KDH.2: 8 residues within 4Å: Chain B: L.38, K.80, V.82, E.83 Chain D: Y.39, E.46 Ligands: KDH.4, KDH.6 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:K.80, B:E.83, B:E.83, D:Y.39, D:Y.39, D:E.46 Hydrophobic interactions: D:Y.39 KDH.3: 5 residues within 4Å: Chain C: L.38, K.80, V.82, E.83 Ligands: KDH.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.80, C:E.83, C:E.83 KDH.4: 5 residues within 4Å: Chain D: L.38, K.80, V.82, E.83 Ligands: KDH.2 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.80, D:E.83, D:E.83 KDH.5: 7 residues within 4Å: Chain A: Y.39, E.46 Chain E: L.38, K.80, V.82, E.83 Ligands: KDH.1 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:K.80, E:E.83, E:E.83, A:Y.39, A:Y.39, A:E.46 KDH.6: 7 residues within 4Å: Chain B: Y.39, E.46 Chain F: L.38, K.80, V.82, E.83 Ligands: KDH.2 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:K.80, F:E.83, F:E.83, B:Y.39, B:Y.39, B:E.46 Hydrophobic interactions: B:Y.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Single-Molecule Insight Into alpha-Synuclein Fibril Structure and Mechanics Modulated by Chemical Compounds. Adv Sci (2025)

Release Date

2025-02-26

Peptides

Alpha-synuclein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
A

E
F

F
B

Alpha-synuclein

Related Entries With Identical Sequence