Crystal structures of highly constrained substrate and hydrolysis products bound to HIV-1 protease. implications for catalytic mechanism

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).

Ligands and binding sites

• DRR · (9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8-[(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxamide · ligand · chains A, B
• SO4 · Sulfate ion · ion · 4 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 · 1813 Ų buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

• 3BXR · Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products Bound To HIV-1… · 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 P03369
• Elsewhere: RCSB PDB 3BXR · PDBe 3BXR · UniProt P03369