Crystal structure analysis of cruzain with three fragments: 1 (N-(1H- benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide), 6 (2-amino- 4,6-difluorobenzothiazole) and 9 (N-(1H-benzimidazol-2-yl)-3-(4- fluorophenyl)-1H-pyrazole-4-carboxamide).

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 26% strand (DSSP).

Ligands and binding sites

• 3H7 · 4,6-difluoro-1,3-benzothiazol-2-amine · ligand · 3 copies · chains B, C, D
• 3H5 · N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide · ligand · 2 copies · chains A, C
• 3H6 · N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide · ligand · chains A

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

Pockets

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

Interfaces

6 interfaces between chains.

• B–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 653 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 640 Ų buried · 8 hydrogen bonds · protein-protein
• D–E · 465 Ų buried · 1 hydrogen bond · protein-protein
• B–E · 297 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide (disulfide).

Compared structures

• 4W5C · Crystal structure analysis of cruzain with three Fragments: 1… · the same entry in another collection · chain E against E, TM-score 1.00
• P25779 · AlphaFold monomer V2.0 prediction for cruzipain (P25779) · a predicted model of the same protein · chain D 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 4W5C · PDBe 4W5C · UniProt P25779