› 3oty

X-ray diffraction
1.75Å resolution

MDR769 HIV-1 protease complexed with RT/RH hepta-peptide

Released:
DOI: 10.2210/pdb3oty/pdb
PDB entry 3oty coloured by chain, front view.
PDB entry 3oty coloured by chain, side view.
PDB entry 3oty coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Nine crystal structures determine the substrate envelope of the MDR HIV-1 protease.
Liu Z, Wang Y, Brunzelle J, Kovari IA, Kovari LC
Protein J 30 173-83 (2011)
PMID: 21394574

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153080 (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: 10.77 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P35963 (Residues: 489-587; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases
p15 Chain: P
Molecule details ›
Chain: P
Length: 7 amino acids
Theoretical weight: 830 Da
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P35963 (Residues: 1025-1031; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P41
Unit cell:
a: 45.576Å b: 45.576Å c: 102.368Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.185 0.236
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

HIV Genome-Wide Protein Associations: a Review of 30 Years of Research.
Li et al. (2016)
2 more

1 mention without citation

Molecular differences between a mutase and a phosphatase: investigations of the activation step in Bacillus cereus phosphopentomutase.
Iverson et al. (2012)