› 3dok

X-ray diffraction
2.9Å resolution

Crystal structure of K103N mutant HIV-1 reverse transcriptase in complex with GW678248.

Released:
DOI: 10.2210/pdb3dok/pdb
PDB entry 3dok coloured by chain, front view.
PDB entry 3dok coloured by chain, side view.
PDB entry 3dok coloured by chain, top view.
Source organism: HIV-1 M:B_HXB2R
Primary publication:
Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors.
Ren J, Chamberlain PP, Stamp A, Short SA, Weaver KL, Romines KR, Hazen R, Freeman A, Ferris RG, Andrews CW, Boone L, Chan JH, Stammers DK
J Med Chem 51 5000-8 (2008)
PMID: 18665583

Function and Biology Details

Reactions catalysed: 
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108511 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pol protein Chain: A
Molecule details ›
Chain: A
Length: 560 amino acids
Theoretical weight: 64.58 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli
UniProt:
  • Canonical: A7YKL0 (Residues: 161-720; Coverage: 56%)
Gene name: pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 440 amino acids
Theoretical weight: 51.38 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli
UniProt:
  • Canonical: P04585 (Residues: 588-1027; Coverage: 31%)
Gene name: gag-pol
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand GWJ 1 x GWJ
1 modified residue:
Ligand CSD 1 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 136.94Å b: 109.77Å c: 72.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.218 0.312
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Dynamic EpCAM expression on circulating and disseminating tumor cells: causes and consequences.
Gires et al. (2014)
2 more

3 mentions without citation

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.
Tarasova et al. (2018)
2 more