› 4y1c

X-ray diffraction
2.3Å resolution

Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain

Released:
DOI: 10.2210/pdb4y1c/pdb
PDB entry 4y1c coloured by chain, front view.
PDB entry 4y1c coloured by chain, side view.
PDB entry 4y1c coloured by chain, top view.
Source organisms:
Entry authors: Wielens J, Chalmers DK

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-146230 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 167 amino acids
Theoretical weight: 18.22 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P12497 (Residues: 1197-1359; Coverage: 11%)
Gene name: gag-pol
Sequence domains: Integrase core domain
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
Cyclic hexapeptide cyc[NdPopPKID] Chain: C
Molecule details ›
Chain: C
Length: 6 amino acids
Theoretical weight: 738 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CD 4 x CD
Ligand SO4 2 x SO4
1 modified residue:
Ligand DIL 1 x DIL

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P212121
Unit cell:
a: 60.48Å b: 61.5Å c: 81.44Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.243 0.295
Expression systems:
  • Escherichia coli K-12
  • Not provided

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