SMTL ID : 8x7m.1

CR-bound E46K alpha-synuclein fibrils

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

16 x YA9: 4-azanyl-3-[(~{E})-[4-[4-[(~{E})-(1-azanyl-4-sulfo-naphthalen-2-yl)diazenyl]phenyl]phenyl]diazenyl]naphthalene-1-sulfonic acid

YA9.1: 10 residues within 4Å: Chain A: A.85, G.86, S.87, I.88, D.98 Chain H: A.85, G.86, I.88, K.96 Ligands: YA9.3 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain A Hydrophobic interactions: H:I.88, A:A.85 Hydrogen bonds: H:G.86, A:A.85 Salt bridges: H:K.96, A:K.96 YA9.2: 4 residues within 4Å: Chain A: K.58, K.60 Ligands: YA9.4, YA9.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.60 Salt bridges: A:K.58 YA9.3: 11 residues within 4Å: Chain A: A.85, G.86, I.88, K.96 Chain B: A.85, G.86, I.88, K.96, D.98 Ligands: YA9.1, YA9.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.85, A:I.88 Hydrogen bonds: B:A.85, A:G.86 Salt bridges: B:K.96, A:K.96 YA9.4: 4 residues within 4Å: Chain B: K.58, K.60 Ligands: YA9.2, YA9.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.58 YA9.5: 10 residues within 4Å: Chain B: A.85, G.86, I.88, K.96 Chain C: A.85, G.86, K.96, D.98 Ligands: YA9.3, YA9.7 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:K.96, B:I.88 Hydrogen bonds: C:G.86, B:G.86 Salt bridges: C:K.96, B:K.96 YA9.6: 3 residues within 4Å: Chain C: K.58, K.60 Ligands: YA9.4 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.58 YA9.7: 7 residues within 4Å: Chain C: I.88, K.96 Chain D: A.85, G.86, K.96, D.98 Ligands: YA9.5 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.88, D:K.96 Salt bridges: C:K.96, D:K.96 Hydrogen bonds: D:G.86, D:G.86 YA9.8: 6 residues within 4Å: Chain E: K.58, K.60 Chain J: K.58, K.60 Ligands: YA9.10, YA9.15 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain J Salt bridges: E:K.58, J:K.58 YA9.9: 11 residues within 4Å: Chain E: A.85, G.86, I.88, K.96, D.98 Chain J: A.85, G.86, I.88, K.96 Ligands: YA9.11, YA9.16 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain J Hydrophobic interactions: E:K.96, J:I.88 Hydrogen bonds: E:A.85, J:G.86 Salt bridges: E:K.96, J:K.96 YA9.10: 4 residues within 4Å: Chain E: K.58, K.60 Chain F: K.58 Ligands: YA9.8 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Salt bridges: E:K.58, F:K.58 YA9.11: 10 residues within 4Å: Chain E: G.86, I.88, K.96 Chain F: A.85, G.86, I.88, K.96, D.98 Ligands: YA9.9, YA9.12 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:I.88, F:K.96 Salt bridges: E:K.96, F:K.96 Hydrogen bonds: F:A.85 YA9.12: 9 residues within 4Å: Chain F: G.86, I.88, K.96 Chain G: A.85, G.86, I.88, K.96, D.98 Ligands: YA9.11 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:I.88, G:I.88, G:K.96 Salt bridges: F:K.96, G:K.96 Hydrogen bonds: G:A.85, G:G.86 YA9.13: 3 residues within 4Å: Chain H: K.58, K.60 Ligands: YA9.2 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:K.60 Salt bridges: H:K.58 YA9.14: 4 residues within 4Å: Chain I: K.58, T.59, K.60 Ligands: YA9.15 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:K.60, I:K.60 Salt bridges: I:K.58 YA9.15: 6 residues within 4Å: Chain I: K.58, K.60 Chain J: K.58, K.60 Ligands: YA9.8, YA9.14 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain J Salt bridges: I:K.58, J:K.58 Hydrophobic interactions: J:K.60, J:K.60 YA9.16: 9 residues within 4Å: Chain I: A.85, G.86, I.88, K.96 Chain J: A.85, G.86, K.96, D.98 Ligands: YA9.9 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:I.88, J:K.96 Hydrogen bonds: I:G.86, J:A.85 Salt bridges: I:K.96, J:K.96

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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