SMTL ID : 8x7b.1

ThT-bound E46K alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

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

TFX.1: 6 residues within 4Å: Chain A: H.50, G.51, V.66 Chain E: H.50, G.51 Ligands: TFX.5 No protein-ligand interaction detected (PLIP) TFX.2: 7 residues within 4Å: Chain C: H.50, G.51, V.66 Chain G: H.50, G.51 Ligands: TFX.3, TFX.9 No protein-ligand interaction detected (PLIP) TFX.3: 6 residues within 4Å: Chain C: H.50, G.51 Chain D: H.50, G.51, V.66 Ligands: TFX.2 No protein-ligand interaction detected (PLIP) TFX.4: 10 residues within 4Å: Chain C: G.86, I.88, K.96 Chain D: K.96 Chain F: G.86, I.88, K.96 Chain G: G.86, I.88, K.96 7 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: C:I.88, C:K.96, F:I.88, G:I.88, G:K.96 pi-Cation interactions: C:K.96, G:K.96 TFX.5: 7 residues within 4Å: Chain E: H.50, G.51, V.66 Chain J: H.50, G.51 Ligands: TFX.1, TFX.12 No protein-ligand interaction detected (PLIP) TFX.6: 9 residues within 4Å: Chain A: K.96 Chain E: I.88, K.96 Chain I: G.86, I.88, K.96 Chain J: G.86, I.88, K.96 9 PLIP interactions: 2 interactions with chain I, 3 interactions with chain E, 4 interactions with chain J Hydrophobic interactions: I:I.88, I:K.96, E:I.88, E:K.96, J:I.88, J:K.96 pi-Cation interactions: E:K.96, J:K.96, J:K.96 TFX.7: 6 residues within 4Å: Chain F: H.50, G.51, V.66 Chain H: H.50, G.51 Ligands: TFX.9 No protein-ligand interaction detected (PLIP) TFX.8: 13 residues within 4Å: Chain C: K.45, K.46, G.47, V.48 Chain F: K.46, G.47, V.48, V.49 Chain G: K.46, G.47, V.48, V.49 Chain H: G.47 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.49 TFX.9: 7 residues within 4Å: Chain F: H.50, G.51 Chain G: H.50, G.51, V.66 Ligands: TFX.2, TFX.7 No protein-ligand interaction detected (PLIP) TFX.10: 4 residues within 4Å: Chain I: H.50, G.51, V.66 Ligands: TFX.12 No protein-ligand interaction detected (PLIP) TFX.11: 12 residues within 4Å: Chain E: K.45, K.46, G.47, V.48 Chain I: K.46, G.47, V.48, V.49 Chain J: K.46, G.47, V.48, V.49 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.49 TFX.12: 7 residues within 4Å: Chain I: H.50, G.51 Chain J: H.50, G.51, V.66 Ligands: TFX.5, TFX.10 No protein-ligand interaction detected (PLIP)

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

2024-11-27

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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