Crystal structure of the binding domain of botulinum neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1A receptors

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 42% strand (DSSP).

Ligands and binding sites

• GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
• SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A
• BGC · beta-D-glucopyranose · sugar
• NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–S · 682 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 6QNS · Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant… · the same entry in another collection · chain A against A, TM-score 1.00
• P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain A against A, TM-score 0.97
• P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain S against A, TM-score 0.64

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P10844
• Every structure of UniProt P21579
• Elsewhere: RCSB PDB 6QNS · PDBe 6QNS · UniProt P10844 · UniProt P21579