SMTL ID : 8zmy.1

F0502B-bound WT polymorph 5a alpha-synuclein fibril

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

15 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: 10 residues within 4Å: Chain A: G.85, A.86, G.87 Chain B: E.84, G.85, I.89 Chain C: I.89, A.91, T.93 Ligands: 1KI.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.89, C:I.89 Hydrogen bonds: B:G.85 1KI.2: 8 residues within 4Å: Chain D: G.85 Chain E: E.84, G.85, I.89 Chain F: I.89, A.91, T.93 Ligands: 1KI.11 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:I.89, E:I.89 1KI.3: 16 residues within 4Å: Chain B: F.5, M.6, K.7 Chain C: F.5, K.7 Chain G: F.5, K.7, G.37 Chain H: F.5, M.6, K.7, E.36, G.37 Chain I: F.5, M.6, K.7 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: C:F.5 Hydrogen bonds: C:K.7, B:K.7, H:K.7 pi-Stacking: B:F.5 1KI.4: 8 residues within 4Å: Chain A: K.11 Chain B: K.11 Chain C: K.11 Chain G: K.11 Chain H: D.3, K.11 Ligands: 1KI.6, 1KI.15 6 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C, 2 interactions with chain G, 2 interactions with chain B Halogen bonds: H:D.3 Hydrophobic interactions: C:K.11, G:K.11, G:K.11, B:K.11, B:K.11 1KI.5: 11 residues within 4Å: Chain B: G.85, A.86, G.87 Chain C: E.84, G.85, I.89 Chain G: I.89, A.91, T.93 Ligands: 1KI.1, 1KI.7 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:I.89, C:I.89 1KI.6: 16 residues within 4Å: Chain A: K.11, A.12, K.13 Chain B: K.11, A.12, K.13 Chain C: K.11, A.12, K.13 Chain G: K.11, A.12, K.13 Chain H: K.11, A.12, K.13 Ligands: 1KI.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:K.13, B:K.13, G:K.13, G:K.13 1KI.7: 9 residues within 4Å: Chain C: G.85, A.86 Chain G: E.84, G.85, I.89 Chain H: I.89, A.91, T.93 Ligands: 1KI.5 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.89 1KI.8: 13 residues within 4Å: Chain B: G.42, S.43 Chain C: G.42, S.43, K.44 Chain G: K.44 Chain H: G.42, S.43, K.44 Chain I: G.42, S.43 Chain K: K.11 Ligands: 1KI.10 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: H:K.44, H:K.44, G:K.44, C:K.44, C:K.44 1KI.9: 19 residues within 4Å: Chain B: X.1, M.2 Chain C: X.1, M.2 Chain E: X.1, M.2 Chain F: X.1, M.2 Chain G: X.1, M.2 Chain H: X.1, M.2 Chain I: X.1, M.2 Chain J: X.1, M.2 Chain K: X.1, M.2 Chain L: M.2 No protein-ligand interaction detected (PLIP) 1KI.10: 8 residues within 4Å: Chain D: K.11 Chain E: K.11 Chain F: K.11 Chain J: K.11 Chain K: D.3, K.11 Ligands: 1KI.8, 1KI.12 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain K, 1 interactions with chain F, 2 interactions with chain J Hydrophobic interactions: E:K.11, E:K.11, F:K.11, J:K.11, J:K.11 Halogen bonds: K:D.3 1KI.11: 9 residues within 4Å: Chain E: G.85 Chain F: E.84, G.85, I.89 Chain J: I.89, A.91, T.93 Ligands: 1KI.2, 1KI.14 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain J Hydrophobic interactions: F:I.89, J:I.89 1KI.12: 13 residues within 4Å: Chain D: K.11, A.12, K.13 Chain E: A.12, K.13 Chain F: K.11, A.12, K.13 Chain J: K.11, A.12, K.13 Chain K: K.13 Ligands: 1KI.10 6 PLIP interactions: 2 interactions with chain E, 3 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: E:K.13, E:K.13, J:K.13, J:K.13 Hydrogen bonds: J:K.13 Halogen bonds: K:K.13 1KI.13: 13 residues within 4Å: Chain E: F.5, M.6, K.7 Chain F: F.5, K.7 Chain J: F.5, K.7 Chain K: F.5, M.6, K.7, G.37 Chain L: M.6, K.7 7 PLIP interactions: 2 interactions with chain J, 1 interactions with chain K, 2 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: J:F.5, F:F.5 Hydrogen bonds: J:K.7, K:K.7, E:K.7, F:K.7 pi-Stacking: E:F.5 1KI.14: 8 residues within 4Å: Chain F: G.85 Chain J: E.84, G.85, I.89 Chain K: I.89, A.91, T.93 Ligands: 1KI.11 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.89 1KI.15: 13 residues within 4Å: Chain E: G.42, S.43 Chain F: G.42, S.43, K.44 Chain J: K.44 Chain K: G.42, S.43, K.44 Chain L: G.42, S.43, K.44 Ligands: 1KI.4 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: F:K.44, F:K.44, K:K.44

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
K

L
L

Alpha-synuclein

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