PDBe 4k4q

X-ray diffraction
1.8Å resolution

TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site

Released:

Function and Biology Details

Reactions catalysed:
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. 
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. 
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.72 KDa
Source organism: Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression system: Escherichia coli
UniProt:
  • Canonical: P12499 (Residues: 490-588; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: I4122
Unit cell:
a: 97.818Å b: 97.818Å c: 98.777Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.23
Expression system: Escherichia coli