HIV protease (pr) dimer with inhibitor tl-3 bound and fragment 2F4 in the OUTSIDE/TOP of flap

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).

Ligands and binding sites

• 3TL · benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate · ligand · chains A, B
• 2FX · 1-benzothiophen-2-ylacetic acid · ligand · chains B
• DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
• BME · Beta-mercaptoethanol · additive · 2 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 · 1822 Ų buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

• 3KFS · HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of… · 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 Q903N5
• Elsewhere: RCSB PDB 3KFS · PDBe 3KFS · UniProt Q903N5