› 5cg6

Hybrid

Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate and isopentenyl pyrophosphate

Released:
DOI: 10.2210/pdb5cg6/pdb
PDB entry 5cg6 coloured by chain, front view.
PDB entry 5cg6 coloured by chain, side view.
PDB entry 5cg6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase.
Yokoyama T, Mizuguchi M, Ostermann A, Kusaka K, Niimura N, Schrader TE, Tanaka I
J Med Chem 58 7549-56 (2015)
PMID: 26314394

Function and Biology Details

Reactions catalysed: 
Prenyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate
Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
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: 355 amino acids
Theoretical weight: 41.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14324 (Residues: 74-419; Coverage: 83%)
Gene names: FDPS, FPS, KIAA1293
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

4 bound ligands:
Ligand MG 3 x MG
Ligand RIS 1 x RIS
Ligand IPE 1 x IPE
Ligand DOD 47 x DOD
No modified residues

Experiments and Validation Details

Experimental Method: X-ray diffraction, Neutron Diffraction
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A, null
Spacegroup: P41212
Unit cell:
a: 111.627Å b: 111.627Å c: 72.553Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.197 0.211
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Neutron protein crystallography: A complementary tool for locating hydrogens in proteins.
O'Dell et al. (2016)
3 more

2 mentions without citation

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition.
Liebschner et al. (2018)
1 more