› 3s3n

X-ray diffraction
2.49Å resolution

Crystal structure of the Prototype Foamy Virus (PFV) S217H mutant intasome in complex with magnesium and Dolutegravir (S/GSK1349572)

Released:
DOI: 10.2210/pdb3s3n/pdb
PDB entry 3s3n coloured by chain, front view.
PDB entry 3s3n coloured by chain, side view.
PDB entry 3s3n coloured by chain, top view.
Source organism: Human spumaretrovirus
Primary publication:
Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572).
Hare S, Smith SJ, Métifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P
Mol Pharmacol 80 565-72 (2011)
PMID: 21719464

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-116861 (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: 44.51 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14350 (Residues: 752-1143; 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: Human spumaretrovirus
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: Human spumaretrovirus
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand ZN 1 x ZN
Ligand SO4 3 x SO4
Ligand GOL 4 x GOL
Ligand NH4 1 x NH4
Ligand MG 2 x MG
Ligand DLU 1 x DLU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P41212
Unit cell:
a: 160.05Å b: 160.05Å c: 123.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.21 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

55 review citations

The structural biology of HIV-1: mechanistic and therapeutic insights.
Engelman et al. (2012)
54 more

5 mentions without citation

Approved Antiviral Drugs over the Past 50 Years.
De Clercq et al. (2016)
4 more