We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

› 2z4v

X-ray diffraction
1.86Å resolution

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and GGPP (inhibitory site)

Released:
DOI: 10.2210/pdb2z4v/pdb
Model geometry
Fit model/data
PDB entry 2z4v coloured by chain, front view.
PDB entry 2z4v coloured by chain, side view.
PDB entry 2z4v coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation.
K-M Chen C, Hudock MP, Zhang Y, Guo RT, Cao R, No JH, Liang PH, Ko TP, Chang TH, Chang SC, Song Y, Axelson J, Kumar A, Wang AH, Oldfield E
J Med Chem 51 5594-607 (2008)
PMID: 18800762

Function and Biology Details

Reactions catalysed: 
isopentenyl diphosphate + dimethylallyl diphosphate = (2E)-geranyl diphosphate + diphosphate.
isopentenyl diphosphate + (2E)-geranyl diphosphate = (2E,6E)-farnesyldiphosphate + diphosphate.
isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate = (2E,6E,10E)-geranylgeranyl diphosphate + diphosphate.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171283 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Geranylgeranyl pyrophosphate synthase BTS1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 340 amino acids
Theoretical weight: 39.3 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12051 (Residues: 1-335; Coverage: 100%)
Gene names: BTS1, YPL069C
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand GRG 2 x GRG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL12B2
Spacegroup: P212121
Unit cell:
a: 47.164Å b: 115.944Å c: 128.404Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.173 0.217
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

12 review citations

The relationship between the chemistry and biological activity of the bisphosphonates.
Ebetino et al. (2011)
11 more

3 mentions without citation

Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy.
Pham et al. (2024)
2 more