Crystal structure of cathepsin S in complex with a nonpeptidic inhibitor (hexagonal spacegroup)

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).

Ligands and binding sites

• H7J · N-[(1S)-1-{1-[(1R,3E)-1-acetylpent-3-en-1-yl]-1H-1,2,3-triazol-4-yl}-1,2-dimethylpropyl]benzamide · ligand · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 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

3 interfaces between chains.

• A–C · 730 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 639 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 293 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide, 3 covalent (disulfide, covalent ligand).

Compared structures

• 2HXZ · Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor (Hexagonal… · the same entry in another collection · chain A against A, TM-score 1.00
• P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 P25774
• Elsewhere: RCSB PDB 2HXZ · PDBe 2HXZ · UniProt P25774