› 4id5

X-ray diffraction
1.95Å resolution

HIV-1 reverse transcriptase with bound fragment at the RNase H primer grip site

Released:
DOI: 10.2210/pdb4id5/pdb
PDB entry 4id5 coloured by chain, front view.
PDB entry 4id5 coloured by chain, side view.
PDB entry 4id5 coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening.
Bauman JD, Patel D, Dharia C, Fromer MW, Ahmed S, Frenkel Y, Vijayan RS, Eck JT, Ho WC, Das K, Shatkin AJ, Arnold E
J Med Chem 56 2738-46 (2013)
PMID: 23342998

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-136840 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 557 amino acids
Theoretical weight: 63.99 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P03366 (Residues: 600-1154; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 429 amino acids
Theoretical weight: 50.1 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P03366 (Residues: 600-1027; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand T27 1 x T27
Ligand DMS 17 x DMS
Ligand 1FF 1 x 1FF
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 162.052Å b: 72.872Å c: 109.153Å
α: 90° β: 100.47° γ: 90°
R-values:
R R work R free
0.188 0.187 0.209
Expression system: Escherichia coli BL21

Quick links

Citations

11 review citations

Twenty years on: the impact of fragments on drug discovery.
Erlanson et al. (2016)
10 more

2 mentions without citation

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