5hbm

X-ray diffraction
3.04Å resolution

Crystal Structure of a Dihydroxycoumarin RNase H Active-Site Inhibitor in Complex with HIV-1 Reverse Transcriptase

Released:
Entry authors: Kirby KA, Sarafianos SG

Function and Biology Details

Reactions catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
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.
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (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(DE3)
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(DE3)
UniProt:
  • Canonical: P03366 (Residues: 600-1027; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Unit cell:
a: 103.931Å b: 69.472Å c: 219.344Å
α: 90° β: 100.62° γ: 90°
R-values:
R R work R free
0.231 0.229 0.274
Expression system: Escherichia coli BL21(DE3)