Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor (WRR483)

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 23% strand (DSSP).

Ligands and binding sites

• 4MC · (Z)-N-(5-guanidino-1-oxo-1-(5-phenyl-1-(phenylsulfonyl)pent-1-en-3-ylamino)pentan-2-yl)-4-methylpiperazine-1-carboxamid E · ligand · 2 copies · chains A, C
• SO4 · Sulfate ion · ion · 7 copies · chains A, C
• EDO · 1,2-ethanediol · additive · 17 copies · chains A, C

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

Pockets

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

Interfaces

1 interface between chains.

• A–C · 635 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 3LXS · Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor (WRR483) · the same entry in another collection · chain A against A, TM-score 1.00
• P25779 · AlphaFold monomer V2.0 prediction for cruzipain (P25779) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P25779
• Elsewhere: RCSB PDB 3LXS · PDBe 3LXS · UniProt P25779