Wild-type HIV-1 protease in complex with a substrate analog ca-P2

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).

Ligands and binding sites

• 0Q4 · N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide · ligand · chains A, B
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 2 copies · chains A, B
• FMT · Formic acid · additive · chains A, B
• GOL · Glycerol · additive · chains 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 · 1887 Ų buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

• 6O48 · Wild-type HIV-1 protease in complex with a substrate analog CA-p2 · the same entry in another collection · chain B against B, 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 6O48 · PDBe 6O48 · UniProt Q5RZ08