SMTL ID : 8k77.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 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: 7 residues within 4Å: Chain A: N.561, N.581 Chain B: F.83, R.194, Y.196, G.422, S.424 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:N.581, B:F.83, B:Y.196 Hydrogen bonds: B:R.194

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

NAG.2: 2 residues within 4Å: Chain A: N.506, G.526 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: D.536, N.556, R.578 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.536, A:D.536, A:R.578

1 x VLX: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide

VLX.4: 8 residues within 4Å: Chain A: I.281, W.308, Y.469, Y.470, V.616, I.671, W.674, D.678 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.281, A:W.308, A:W.308, A:Y.469, A:V.616, A:I.671, A:W.674 Hydrogen bonds: A:Y.470, A:D.678

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: A
Botulinum neurotoxin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

Botulinum neurotoxin

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