› 1zpk

X-ray diffraction
1.65Å resolution

Crystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2

Released:
DOI: 10.2210/pdb1zpk/pdb
PDB entry 1zpk coloured by chain, front view.
PDB entry 1zpk coloured by chain, side view.
PDB entry 1zpk coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Entry authors: Duskova J, Skalova T, Dohnalek J, Petrokova H, Hasek J

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136867 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase A2 domain-containing protein; Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.9 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7ZCL6 (Residues: 1-99; Coverage: 100%)
  • Canonical: P03367 (Residues: 501-599; Coverage: 7%)
Gene names: gag-pol, pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

3 bound ligands:
Ligand 0ZS 1 x 0ZS
Ligand CL 1 x CL
Ligand NA 1 x NA
1 modified residue:
Ligand CME 2 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P61
Unit cell:
a: 62.483Å b: 62.483Å c: 82.412Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.159 0.156 0.253
Expression system: Escherichia coli BL21(DE3)

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