SMTL ID : 8zlo.1

F0502B-bound E46K alpha-synuclein fibril

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

10 x 1KI: 2-bromanyl-4-[(~{E})-2-[6-[2-(2-fluoranylethoxy)ethyl-methyl-amino]-5-methyl-1,3-benzothiazol-2-yl]ethenyl]phenol

1KI.1: 8 residues within 4Å: Chain A: H.6, G.7, V.8 Chain E: K.53, Q.55 Chain I: H.6 Ligands: 1KI.9, 1KI.10 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain I, 1 interactions with chain E Hydrogen bonds: A:H.6, A:V.8, I:H.6, E:Q.55 1KI.2: 8 residues within 4Å: Chain C: H.6, G.7, V.8 Chain F: K.53, Q.55 Chain G: H.6 Ligands: 1KI.5, 1KI.6 4 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C, 1 interactions with chain F Hydrogen bonds: G:H.6, C:H.6, C:V.8, F:Q.55 1KI.3: 19 residues within 4Å: Chain C: G.42, I.44, F.50, K.52 Chain D: G.42, I.44, K.52 Chain F: G.42, I.44, K.52 Chain G: G.42, I.44, K.52 Chain H: G.42, S.43, I.44, K.52 Chain K: G.42, I.44 13 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F, 5 interactions with chain G, 1 interactions with chain D, 2 interactions with chain H, 1 interactions with chain K Hydrophobic interactions: C:F.50, C:K.52, F:I.44, F:K.52, G:I.44, G:K.52, H:I.44 Hydrogen bonds: G:K.52, H:K.52 pi-Cation interactions: G:K.52, G:K.52 Halogen bonds: D:G.42, K:G.42 1KI.4: 17 residues within 4Å: Chain C: K.2, G.3, V.11 Chain D: K.2 Chain F: K.1, G.3, V.11 Chain G: K.1, K.2, G.3, V.11 Chain H: K.1, K.2, G.3, V.11 Chain K: K.1, G.3 7 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H, 1 interactions with chain G, 1 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: F:K.1, F:V.11, H:K.1, H:V.11, G:K.1, K:K.1 Halogen bonds: D:K.2 1KI.5: 7 residues within 4Å: Chain C: H.6 Chain D: H.6, G.7, V.8 Chain G: K.53, Q.55 Ligands: 1KI.2 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:Q.55, D:H.6 1KI.6: 7 residues within 4Å: Chain F: H.6 Chain G: H.6, G.7, V.8 Chain H: K.53, Q.55 Ligands: 1KI.2 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:H.6, H:Q.55 1KI.7: 17 residues within 4Å: Chain A: G.42, I.44, F.50, K.52 Chain B: K.52 Chain E: G.42, I.44, K.52 Chain I: G.42, I.44, K.52 Chain J: G.42, S.43, I.44, K.52 Chain L: G.42, I.44 13 PLIP interactions: 2 interactions with chain E, 2 interactions with chain J, 3 interactions with chain A, 5 interactions with chain I, 1 interactions with chain L Hydrophobic interactions: E:I.44, E:K.52, J:I.44, A:F.50, A:K.52, I:I.44, I:K.52 Hydrogen bonds: J:K.52, A:K.52, I:K.52 pi-Cation interactions: I:K.52, I:K.52 Halogen bonds: L:G.42 1KI.8: 17 residues within 4Å: Chain A: K.2, G.3, V.11 Chain B: K.2 Chain E: K.1, G.3, V.11 Chain I: K.1, K.2, G.3, V.11 Chain J: K.1, K.2, G.3, V.11 Chain L: K.1, G.3 7 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain B, 2 interactions with chain E, 2 interactions with chain J Hydrophobic interactions: L:K.1, I:K.1, E:K.1, E:V.11, J:K.1, J:V.11 Halogen bonds: B:K.2 1KI.9: 7 residues within 4Å: Chain A: H.6 Chain B: H.6, G.7, V.8 Chain I: K.53, Q.55 Ligands: 1KI.1 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain B Hydrogen bonds: I:Q.55, B:H.6 1KI.10: 7 residues within 4Å: Chain E: H.6 Chain I: H.6, G.7, V.8 Chain J: K.53, Q.55 Ligands: 1KI.1 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Q.55, I:H.6

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: ABCDEFGHIJKL

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

K
O

L
T

Alpha-synuclein

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