› 2aof

X-ray diffraction
1.32Å resolution

Crystal structure analysis of HIV-1 Protease mutant V82A with a substrate analog P1-P6

Released:
DOI: 10.2210/pdb2aof/pdb
PDB entry 2aof coloured by chain, front view.
PDB entry 2aof coloured by chain, side view.
PDB entry 2aof coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs.
Tie Y, Boross PI, Wang YF, Gaddis L, Liu F, Chen X, Tozser J, Harrison RW, Weber IT
FEBS J 272 5265-77 (2005)
PMID: 16218957

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
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 domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138028 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.71 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04587 (Residues: 501-599; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases
PEPTIDE INHIBITOR Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.14 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand NA 1 x NA
Ligand CL 2 x CL
Ligand ACY 1 x ACY
1 modified residue:
Ligand FRD 1 x FRD

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P21212
Unit cell:
a: 58.457Å b: 85.851Å c: 46.394Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.134 0.131 0.184
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

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

1 mention without citation

Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs.
Tie et al. (2005)