SMTL ID : 8jlh.1

Cryo-EM structure of SV2A dimer in complex with BoNT/A2 Hc and levetiracetam

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: N.561, I.580, N.581 Chain B: F.83, R.194, Y.196, G.422, S.424 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.581, B:F.83, B:Y.196 NAG-NAG-FUC.2: 7 residues within 4Å: Chain C: N.561, I.580, N.581 Chain D: F.83, R.194, G.422, S.424 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:N.581, D:F.83

1 x UKX: (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide

UKX.3: 6 residues within 4Å: Chain A: I.281, W.308, Y.469, Y.470, W.674, D.678 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.281, A:W.308, A:W.308, A:W.308, A:Y.469 Hydrogen bonds: A:D.678, A:K.702

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: N.506, I.525, G.526 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.506 NAG.5: 2 residues within 4Å: Chain A: D.536, N.556 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.536 Hydrogen bonds: A:D.536 NAG.6: 3 residues within 4Å: Chain C: N.506, I.525, G.526 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.506 NAG.7: 2 residues within 4Å: Chain C: D.536, N.556 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamagata, A. et al., Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Nat Commun (2024)

Release Date

2024-05-01

Peptides

Synaptic vesicle glycoprotein 2A: AC
Botulinum neurotoxin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Synaptic vesicle glycoprotein 2A

Botulinum neurotoxin

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