SMTL ID : 8x7o.1

PiB-bound E46K mutanted alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

12 x IZV: 2-[4-(methylamino)phenyl]-1,3-benzothiazol-6-ol(Non-covalent)

IZV.1: 2 residues within 4Å: Chain A: H.50 Chain B: H.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.50 IZV.2: 8 residues within 4Å: Chain A: I.88, K.96 Chain B: K.96 Chain E: I.88, K.96 Chain J: G.86, I.88, K.96 9 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A, 2 interactions with chain J Hydrophobic interactions: E:K.96, A:I.88, A:K.96, J:I.88 Hydrogen bonds: E:K.96, J:K.96 pi-Cation interactions: E:K.96, E:K.96, A:K.96 IZV.3: 3 residues within 4Å: Chain C: H.50 Chain D: H.50, V.66 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.66 Hydrogen bonds: C:H.50 IZV.4: 1 residues within 4Å: Chain D: H.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.50 IZV.5: 7 residues within 4Å: Chain C: I.88, K.96 Chain D: I.88, K.96 Chain G: G.86, I.88, K.96 10 PLIP interactions: 2 interactions with chain G, 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: G:I.88, D:I.88, D:K.96, C:I.88, C:K.96 Hydrogen bonds: G:K.96, C:K.96 pi-Cation interactions: D:K.96, C:K.96, C:K.96 IZV.6: 2 residues within 4Å: Chain A: H.50 Chain E: H.50 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.50 IZV.7: 2 residues within 4Å: Chain F: H.50 Chain G: H.50 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.50 IZV.8: 2 residues within 4Å: Chain C: H.50 Chain G: H.50 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.50 IZV.9: 14 residues within 4Å: Chain C: K.46, G.47, V.48, V.49, V.55 Chain D: K.46, G.47, V.49, V.55 Chain F: G.47 Chain G: K.46, G.47, V.48, V.49 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:V.49, D:V.55, D:V.55, G:V.49 IZV.10: 2 residues within 4Å: Chain I: H.50 Chain J: H.50 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:H.50 IZV.11: 2 residues within 4Å: Chain E: H.50 Chain J: H.50 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:H.50 IZV.12: 14 residues within 4Å: Chain A: K.46, G.47, V.49, V.55 Chain E: K.46, G.47, V.49, V.55 Chain I: G.47 Chain J: K.46, G.47, V.48, V.49, V.55 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: A:V.49, A:V.55, A:V.55, J:V.49, E:V.49 Hydrogen bonds: A:G.47

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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