› 2yng

X-ray diffraction
2.12Å resolution

HIV-1 Reverse Transcriptase in complex with inhibitor GSK560

Released:
DOI: 10.2210/pdb2yng/pdb
PDB entry 2yng coloured by chain, front view.
PDB entry 2yng coloured by chain, side view.
PDB entry 2yng coloured by chain, top view.
Source organism: HIV-1 M:B_HXB2R
Primary publication:
Rational design of potent non-nucleoside inhibitors of HIV-1 reverse transcriptase.
Chong P, Sebahar P, Youngman M, Garrido D, Zhang H, Stewart EL, Nolte RT, Wang L, Ferris RG, Edelstein M, Weaver K, Mathis A, Peat A
J Med Chem 55 10601-9 (2012)
PMID: 23137340

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138005 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 563 amino acids
Theoretical weight: 64.9 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 588-1147; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 447 amino acids
Theoretical weight: 52.24 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 588-1015; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand SRT 1 x SRT
Ligand WHU 1 x WHU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 118.876Å b: 154.627Å c: 156.958Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Comprehensive review in current developments of imidazole-based medicinal chemistry.
Zhang et al. (2014)
6 more

5 mentions without citation

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