High-resolution crystal structure of the P-I snake venom metalloproteinase BAP1 in complex with a peptidomimetic: insights into inhibitor binding

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Ligands and binding sites

• WR2 · (2R,3R)-N^1^-[(1S)-2,2-dimethyl-1-(methylcarbamoyl)propyl]-N^4^-hydroxy-2-(2-methylpropyl)-3-{[(1,3-thiazol-2-ylcarbonyl)amino]methyl}butanediamide · ligand · chains A
• ZN · Zinc ion · metal · chains A
• GOL · Glycerol · additive · chains A
• IMD · Imidazole · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, cyclization).

Compared structures

• 2W14 · High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in… · the same entry in another collection · chain A against A, TM-score 1.00
• P83512 · AlphaFold monomer V2.0 prediction for snake venom metalloproteinase BAP1 (P83512) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P83512
• Elsewhere: RCSB PDB 2W14 · PDBe 2W14 · UniProt P83512