› 5frn

X-ray diffraction
2.85Å resolution

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ419 (compound 4c)

Released:
DOI: 10.2210/pdb5frn/pdb
PDB entry 5frn coloured by chain, front view.
PDB entry 5frn coloured by chain, side view.
PDB entry 5frn coloured by chain, top view.
Source organisms:
Primary publication:
HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases.
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR
OpenAccess logo ACS Chem Biol 11 1074-81 (2016)
PMID: 26808478

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-509436 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 395 amino acids
Theoretical weight: 44.46 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14350 (Residues: 754-1143; Coverage: 34%)
Gene name: pol
Sequence domains:
Structure domains:
5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.83 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP *AP*CP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.2 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 2 x MG
Ligand GOL 6 x GOL
Ligand SO4 5 x SO4
Ligand QUW 1 x QUW
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P41212
Unit cell:
a: 159.89Å b: 159.89Å c: 123.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.178 0.2
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Retroviral DNA Integration.
Lesbats et al. (2016)
4 more

4 mentions without citation

Structural Biology of HIV Integrase Strand Transfer Inhibitors.
Jóźwik et al. (2020)
3 more