SMTL ID : 9f2b.1

Focused refinement of SV2B luminal domain and BoNT/A1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.49 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 7 residues within 4Å: Chain A: H.451, D.471, T.472, F.473, N.491, T.493, R.513 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.471, A:T.472, A:T.493, A:R.513, A:R.513

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

NAG-NAG-BMA-MAN-FUC.2: 4 residues within 4Å: Chain A: I.515, N.516 Chain B: N.971, H.1081 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.1081

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

NAG.3: 1 residues within 4Å: Chain A: N.441 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khanppnavar, B. et al., Cryo-EM structure of the botulinum neurotoxin A/SV2B complex and its implications for translocation. Nat Commun (2025)

Release Date

2025-03-12

Peptides

Synaptic vesicle glycoprotein 2B: A
Botulinum neurotoxin type A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Synaptic vesicle glycoprotein 2B

Botulinum neurotoxin type A

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