› 3dlk

X-ray diffraction
1.85Å resolution

Crystal Structure of an engineered form of the HIV-1 Reverse Transcriptase, RT69A

Released:
DOI: 10.2210/pdb3dlk/pdb
PDB entry 3dlk coloured by chain, front view.
PDB entry 3dlk coloured by chain, side view.
PDB entry 3dlk coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
Bauman JD, Das K, Ho WC, Baweja M, Himmel DM, Clark AD, Oren DA, Boyer PL, Hughes SH, Shatkin AJ, Arnold E
Nucleic Acids Res 36 5083-92 (2008)
PMID: 18676450

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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136840 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 556 amino acids
Theoretical weight: 63.95 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 599-1154; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 423 amino acids
Theoretical weight: 49.53 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 605-1027; Coverage: 29%)
Gene name: gag-pol
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 164.01Å b: 72.04Å c: 109.33Å
α: 90° β: 104.38° γ: 90°
R-values:
R R work R free
0.237 0.237 0.25
Expression system: Escherichia coli

Quick links

Citations

6 review citations

HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design.
Zhan et al. (2013)
5 more

17 mentions without citation

Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
Bauman et al. (2008)
16 more