PDBe 3dox

X-ray diffraction
2Å resolution

X-ray structure of HIV-1 protease in situ product complex

Released:
Primary publication:
X-ray structure of HIV-1 protease in situ product complex.
Proteins 74 594-602 (2009)
PMID: 18704947

Function and Biology Details

Reactions catalysed:
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. 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). 
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Protease Chain: A
Molecule details ›
Chain: A
Length: 203 amino acids
Theoretical weight: 21.9 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli
UniProt:
  • Canonical: P04585 (Residues: 489-587; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases
A PEPTIDE SUBSTRATE-PIV Chain: Q
Molecule details ›
Chain: Q
Length: 3 amino acids
Theoretical weight: 327 Da
Source organism: Synthetic construct
Expression system: Not provided
A PEPTIDE SUBSTRATE-SQNY Chain: P
Molecule details ›
Chain: P
Length: 4 amino acids
Theoretical weight: 510 Da
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P61
Unit cell:
a: 62.38Å b: 62.38Å c: 82Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.197 0.236
Expression systems:
  • Escherichia coli
  • Not provided