SMTL ID : 9o4b.1

Cryo-EM structure of in-vitro alpha-synuclein fibril bound with Exemplar-6 PET-radioligand

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.59 Å

Oligo State

homo-12-mer

Ligands

12 x 01: 2-(3,4-dimethylphenoxy)-N-[3-(4-fluorophenyl)-1,2-oxazol-5-yl]acetamide

01.1: 8 residues within 4Å: Chain A: Y.39, K.43, K.45 Chain B: K.45, H.50 Chain G: K.58 Chain H: K.58 Ligands: 01.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.39, A:Y.39, A:K.45 Hydrogen bonds: A:K.43 01.2: 5 residues within 4Å: Chain A: K.58 Chain B: K.58 Chain G: K.45, H.50 Ligands: 01.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.58 01.3: 7 residues within 4Å: Chain B: K.43, K.45 Chain C: K.45 Chain H: K.58 Chain I: K.58 Ligands: 01.1, 01.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.43 Hydrogen bonds: B:K.43 01.4: 9 residues within 4Å: Chain C: Y.39, K.43, K.45 Chain D: K.45, H.50 Chain I: K.58 Chain J: K.58 Ligands: 01.3, 01.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.39, C:Y.39, C:K.45 Hydrogen bonds: C:K.43 01.5: 8 residues within 4Å: Chain D: Y.39, K.43, K.45 Chain E: K.45 Chain J: K.58 Chain K: K.58 Ligands: 01.4, 01.6 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.39, D:K.43 Hydrogen bonds: D:K.43 01.6: 8 residues within 4Å: Chain E: Y.39, K.43, K.45 Chain F: K.45 Chain K: K.58 Chain L: K.58 Ligands: 01.5, 01.7 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.39, E:Y.39, E:K.43, E:K.45 Hydrogen bonds: E:K.43 01.7: 4 residues within 4Å: Chain F: K.43, K.45 Chain L: K.58 Ligands: 01.6 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.43 Hydrogen bonds: F:K.43 01.8: 7 residues within 4Å: Chain B: K.58 Chain C: K.58 Chain G: K.43, K.45 Chain H: K.45 Ligands: 01.2, 01.9 No protein-ligand interaction detected (PLIP) 01.9: 8 residues within 4Å: Chain C: K.58 Chain D: K.58 Chain H: K.43, K.45 Chain I: K.45, H.50 Ligands: 01.8, 01.10 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:K.45 Hydrogen bonds: C:K.58 01.10: 7 residues within 4Å: Chain D: K.58 Chain E: K.58 Chain I: K.43, K.45 Chain J: K.45 Ligands: 01.9, 01.11 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:K.43 01.11: 8 residues within 4Å: Chain E: K.58 Chain F: K.58 Chain J: K.43, K.45 Chain K: K.45, H.50 Ligands: 01.10, 01.12 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.58 01.12: 5 residues within 4Å: Chain F: K.58 Chain K: K.43, K.45 Chain L: K.45 Ligands: 01.11 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:K.43 Hydrogen bonds: K:K.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanchez, J.C. et al., Complementary Structural and Chemical Biology Methods Reveal the Basis for Selective Radioligand Binding to Alpha-Synuclein in MSA Tissue. To Be Published

Release Date

2025-04-23

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

Related Entries With Identical Sequence