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X-ray diffraction
2.47Å resolution

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound

Released:
DOI: 10.2210/pdb3ldw/pdb
PDB entry 3ldw coloured by chain, front view.
PDB entry 3ldw coloured by chain, side view.
PDB entry 3ldw coloured by chain, top view.
Source organism: Plasmodium vivax Sal-1
Primary publication:
Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites.
Artz JD, Wernimont AK, Dunford JE, Schapira M, Dong A, Zhao Y, Lew J, Russell RG, Ebetino FH, Oppermann U, Hui R
J Biol Chem 286 3315-22 (2011)
PMID: 21084289

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107670 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Farnesyl pyrophosphate synthase, putative Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 396 amino acids
Theoretical weight: 46.22 KDa
Source organism: Plasmodium vivax Sal-1
Expression system: Escherichia coli
UniProt:
  • Canonical: A5K4U6 (Residues: 1-375; Coverage: 100%)
Gene name: PVX_092040
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

5 bound ligands:
Ligand ZOL 4 x ZOL
Ligand IPE 4 x IPE
Ligand MG 12 x MG
Ligand EDO 2 x EDO
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 111.264Å b: 139.543Å c: 109.711Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.239 0.286
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Bisphosphonates: the first 40 years.
Russell RG. (2011)
8 more

4 mentions without citation

Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.
No et al. (2012)
3 more