› 4nfi

X-ray diffraction
1.85Å resolution

Crystal structure of human FPPS in complex with magnesium and JDS05120

Released:
DOI: 10.2210/pdb4nfi/pdb
PDB entry 4nfi coloured by chain, front view.
PDB entry 4nfi coloured by chain, side view.
PDB entry 4nfi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase.
Park J, Rodionov D, De Schutter JW, Lin YS, Tsantrizos YS, Berghuis AM
PLoS One 12 e0186447 (2017)
PMID: 29036218

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: F
Molecule details ›
Chain: F
Length: 375 amino acids
Theoretical weight: 43.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14324 (Residues: 67-419; Coverage: 84%)
Gene names: FDPS, FPS, KIAA1293
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

2 bound ligands:
Ligand JD5 1 x JD5
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P41212
Unit cell:
a: 110.51Å b: 110.51Å c: 66.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.196
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Phosphonate and Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthases: A Structure-Guided Perspective.
Park et al. (2020)
1 other article

1 mention without citation

Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase.
Park et al. (2017)