SMTL ID : 7ynm.1

ThT-bound alpha-synuclein fibrils conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x TFX: 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium(Non-covalent)

TFX.1: 9 residues within 4Å: Chain A: K.80, V.82 Chain C: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.2, TFX.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.82, C:Y.39, C:Y.39 TFX.2: 6 residues within 4Å: Chain A: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.39, A:Y.39 TFX.3: 8 residues within 4Å: Chain B: K.80, V.82 Chain D: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.4 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.39, D:Y.39, B:V.82 TFX.4: 9 residues within 4Å: Chain B: Y.39, E.46, K.80, T.81, V.82 Chain H: K.80, V.82 Ligands: TFX.3, TFX.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:Y.39, B:Y.39, H:V.82 TFX.5: 8 residues within 4Å: Chain E: K.80, V.82 Chain G: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.6 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:Y.39, G:Y.39, E:V.82 TFX.6: 9 residues within 4Å: Chain C: K.80, V.82 Chain E: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.1, TFX.5 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:V.82, E:Y.39, E:Y.39 TFX.7: 9 residues within 4Å: Chain F: K.80, V.82 Chain H: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.4, TFX.8 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: F:V.82, H:Y.39, H:Y.39 TFX.8: 6 residues within 4Å: Chain F: Y.39, E.46, K.80, T.81, V.82 Ligands: TFX.7 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.39, F:Y.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tao, Y.Q. et al., ThT-bound alpha-synuclein fibrils conformation 1. To Be Published

Release Date

2023-08-02

Peptides

Alpha-synuclein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

F
H

G
I

H
J

Alpha-synuclein

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