› 4p0v

X-ray diffraction
2.4Å resolution

Crystal structure of human farnesyl diphosphoate synthase in complex with zoledronate and taxodione

Released:
DOI: 10.2210/pdb4p0v/pdb
PDB entry 4p0v coloured by chain, front view.
PDB entry 4p0v coloured by chain, side view.
PDB entry 4p0v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site.
Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E
Proc Natl Acad Sci U S A 111 E2530-9 (2014)
PMID: 24927548

Function and Biology Details

Reactions catalysed: 
Prenyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate
Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146902 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Farnesyl pyrophosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 39.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14324 (Residues: 73-419; Coverage: 83%)
Gene names: FDPS, FPS, KIAA1293
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

3 bound ligands:
Ligand ZOL 1 x ZOL
Ligand 1WO 1 x 1WO
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P41212
Unit cell:
a: 112.143Å b: 112.143Å c: 67.053Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.202 0.292
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Computational methods in drug discovery.
Leelananda et al. (2016)
2 more

2 mentions without citation

A Guide to In Silico Drug Design.
Chang et al. (2022)
1 more