› 3wnh

X-ray diffraction
1.5Å resolution

Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase

Released:
DOI: 10.2210/pdb3wnh/pdb
PDB entry 3wnh coloured by chain, front view.
PDB entry 3wnh coloured by chain, side view.
PDB entry 3wnh coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Entry authors: Wielens J, Chalmers DK, Parker MW

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146229 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 157 amino acids
Theoretical weight: 17.1 KDa
Source organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Expression system: Escherichia coli
UniProt:
  • Canonical: P12497 (Residues: 1203-1359; Coverage: 11%)
Gene name: gag-pol
Sequence domains: Integrase core domain
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
PK(NLE)DN(DVA) peptide Chains: C, D
Molecule details ›
Chains: C, D
Length: 6 amino acids
Theoretical weight: 686 Da
Source organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CD 4 x CD
Ligand CL 2 x CL
Ligand SO4 6 x SO4
2 modified residues:
Ligand NLE 2 x NLE
Ligand DVA 2 x DVA

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P32
Unit cell:
a: 49.44Å b: 49.44Å c: 101.33Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.19 0.227
Expression systems:
  • Escherichia coli
  • Not provided

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