SMTL ID : 8x7r.1

C05-03-bound E46K alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

20 x Y9W: 2-[(~{E})-4-[6-(methylamino)pyridin-3-yl]but-1-en-3-ynyl]-1,3-benzothiazol-6-ol

Y9W.1: 16 residues within 4Å: Chain A: K.46, G.47, V.48, V.49, V.55 Chain B: G.47, V.55 Chain C: K.46, G.47, V.48, V.49, V.55 Chain D: K.46, G.47, V.55 Chain H: G.47 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: B:V.55, D:V.55, D:V.55, C:V.55 Y9W.2: 5 residues within 4Å: Chain A: H.50, G.51, Q.99 Chain B: H.50, G.51 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.50, A:G.51, A:Q.99 Y9W.3: 2 residues within 4Å: Chain A: K.60 Chain J: E.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:K.60 Y9W.4: 2 residues within 4Å: Chain B: E.83 Chain J: K.60 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:K.60, J:K.60 Y9W.5: 6 residues within 4Å: Chain B: H.50, G.51, V.52, Q.99 Chain C: H.50, G.51 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.52 Hydrogen bonds: B:G.51, B:Q.99, C:H.50 Y9W.6: 4 residues within 4Å: Chain C: E.83, G.84, A.85 Chain E: K.60 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.60, E:K.60 Y9W.7: 6 residues within 4Å: Chain C: H.50, G.51, V.52, Q.99 Chain D: H.50, G.51 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.52 Hydrogen bonds: C:H.50, C:G.51, C:Q.99, D:H.50 Y9W.8: 9 residues within 4Å: Chain A: I.88, K.96 Chain B: I.88, K.96 Chain C: I.88, K.96 Chain D: I.88, K.96 Chain H: G.86 8 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: D:K.96, C:I.88, B:I.88 Hydrogen bonds: D:K.96, C:K.96, A:K.96 pi-Cation interactions: D:K.96, C:K.96 Y9W.9: 4 residues within 4Å: Chain D: E.83, G.84, A.85 Chain F: K.60 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.60, F:K.60 Y9W.10: 15 residues within 4Å: Chain E: K.46, G.47, V.48, V.49, V.55 Chain F: K.46, G.47, V.55 Chain I: K.46, G.47, V.48, V.49, V.55 Chain J: G.47, V.55 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: J:V.55, E:V.55, F:V.55 Y9W.11: 5 residues within 4Å: Chain E: H.50, G.51, V.52 Chain F: H.50, G.51 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:V.52 Hydrogen bonds: E:G.51, E:Q.99, F:H.50 Y9W.12: 2 residues within 4Å: Chain B: K.60 Chain E: E.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.60, B:K.60 Y9W.13: 4 residues within 4Å: Chain C: K.60 Chain F: E.83, G.84, A.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.60, C:K.60 Y9W.14: 9 residues within 4Å: Chain E: I.88, K.96 Chain F: I.88, K.96 Chain G: I.88, K.96 Chain I: G.86 Chain J: I.88, K.96 8 PLIP interactions: 1 interactions with chain E, 3 interactions with chain G, 3 interactions with chain F, 1 interactions with chain J Hydrophobic interactions: E:I.88, G:K.96, F:I.88, F:K.96 Hydrogen bonds: G:K.96, F:K.96, J:K.96 pi-Cation interactions: G:K.96 Y9W.15: 4 residues within 4Å: Chain D: K.60 Chain G: E.83, G.84, A.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.60, D:K.60 Y9W.16: 5 residues within 4Å: Chain A: H.50, G.51 Chain H: H.50, G.51, Q.99 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:H.50, H:Q.99, A:H.50 Y9W.17: 5 residues within 4Å: Chain I: H.50, G.51, Q.99 Chain J: H.50, G.51 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:G.51, I:Q.99, J:H.50 Y9W.18: 2 residues within 4Å: Chain A: E.83 Chain I: K.60 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.60, I:K.60 Y9W.19: 2 residues within 4Å: Chain I: H.50, G.51 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.50, I:G.51 Y9W.20: 6 residues within 4Å: Chain E: H.50, G.51 Chain J: H.50, G.51, V.52, Q.99 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain J Hydrogen bonds: E:H.50, J:G.51, J:Q.99 Hydrophobic interactions: J:V.52

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
F

B
G

C
C

D
D

E
E

F
A

G
B

H
H

I
I

J
J

Alpha-synuclein

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