X-ray crystal structure of bpi-11 HIV-1 protease complex

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).

Ligands and binding sites

• B0F · (4R)-3-[(2S,3S)-3-[2-[4-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide · ligand · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• CL · Chloride ion · ion · chains B
• GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1844 Ų buried · 36 hydrogen bonds · protein-protein

Compared structures

• 6IXD · X-ray crystal structure of bPI-11 hiv-1 protease complex · the same entry in another collection · chain A 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 Q5RZ08
• Elsewhere: RCSB PDB 6IXD · PDBe 6IXD · UniProt Q5RZ08