› 4kb9

X-ray diffraction
1.29Å resolution

Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A

Released:
DOI: 10.2210/pdb4kb9/pdb
PDB entry 4kb9 coloured by chain, front view.
PDB entry 4kb9 coloured by chain, side view.
PDB entry 4kb9 coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Highly potent HIV-1 protease inhibitors with novel tricyclic P2 ligands: design, synthesis, and protein-ligand X-ray studies.
Ghosh AK, Parham GL, Martyr CD, Nyalapatla PR, Osswald HL, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H
J Med Chem 56 6792-802 (2013)
PMID: 23947685

Function and Biology Details

Reaction catalysed: 
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181991 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase A2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.74 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7SSI0 (Residues: 1-99; Coverage: 100%)
Gene name: pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

5 bound ligands:
Ligand G79 1 x G79
Ligand CL 2 x CL
Ligand ACT 3 x ACT
Ligand NA 1 x NA
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21212
Unit cell:
a: 58.477Å b: 86.3Å c: 46.045Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.142 0.139 0.18
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS.
Ghosh et al. (2016)
1 more

2 mentions without citation

Highly potent HIV-1 protease inhibitors with novel tricyclic P2 ligands: design, synthesis, and protein-ligand X-ray studies.
Ghosh et al. (2013)
1 more