› 2hny

X-ray diffraction
2.5Å resolution

Crystal Structure of E138K Mutant HIV-1 Reverse Transcriptase in Complex with Nevirapine

Released:
DOI: 10.2210/pdb2hny/pdb
PDB entry 2hny coloured by chain, front view.
PDB entry 2hny coloured by chain, side view.
PDB entry 2hny coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138.
Ren J, Nichols CE, Stamp A, Chamberlain PP, Ferris R, Weaver KL, Short SA, Stammers DK
FEBS J 273 3850-60 (2006)
PMID: 16911530

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-136858 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 534 amino acids
Theoretical weight: 61.92 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P04585 (Residues: 591-1124; Coverage: 37%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 422 amino acids
Theoretical weight: 49.45 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03367 (Residues: 606-1027; Coverage: 29%)
Gene name: gag-pol
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PO4 3 x PO4
Ligand MG 1 x MG
Ligand NVP 1 x NVP
1 modified residue:
Ligand CSD 1 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 139.6Å b: 115Å c: 65.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.284
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase.
Ren et al. (2008)
4 more

9 mentions without citation

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