HIV-1 Protease Saquinavir:Ritonavir 1:5 complex structure

Structure

x-ray diffraction · resolution 1.25 · 1 distinct chain · 4% helix, 56% strand (DSSP).

Ligands and binding sites

• ROC · (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide · ligand · 2 copies · chains A, B, C, D
• NA · Sodium ion · metal · 3 copies · chains A, B
• CL · Chloride ion · ion · 6 copies · chains A, B, C
• DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B, C, D
• ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 3 copies · chains A, B, D, C

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 1842 Ų buried · 36 hydrogen bonds · protein-protein
• A–B · 1838 Ų buried · 33 hydrogen bonds · protein-protein
• B–D · 292 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 168 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 3NDU · HIV-1 protease SAQUINAVIR:RITONAVIR 1:5 complex structure · 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 Q7SSI0
• Elsewhere: RCSB PDB 3NDU · PDBe 3NDU · UniProt Q7SSI0