› 3dyg

X-ray diffraction
2.1Å resolution

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461

Released:
DOI: 10.2210/pdb3dyg/pdb
PDB entry 3dyg coloured by chain, front view.
PDB entry 3dyg coloured by chain, side view.
PDB entry 3dyg coloured by chain, top view.
Source organism: Trypanosoma brucei
Primary publication:
Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation.
Zhang Y, Cao R, Yin F, Hudock MP, Guo RT, Krysiak K, Mukherjee S, Gao YG, Robinson H, Song Y, No JH, Bergan K, Leon A, Cass L, Goddard A, Chang TK, Lin FY, Van Beek E, Papapoulos S, Wang AH, Kubo T, Ochi M, Mukkamala D, Oldfield E
J Am Chem Soc 131 5153-62 (2009)
PMID: 19309137

Function and Biology Details

Reaction catalysed: 
Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183122 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Farnesyl pyrophosphate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 390 amino acids
Theoretical weight: 44.48 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86C09 (Residues: 1-367; Coverage: 100%)
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

5 bound ligands:
Ligand MG 6 x MG
Ligand ACT 2 x ACT
Ligand NI9 2 x NI9
Ligand BME 2 x BME
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: C2
Unit cell:
a: 135.565Å b: 118.52Å c: 63.186Å
α: 90° β: 112.36° γ: 90°
R-values:
R R work R free
0.207 0.207 0.25
Expression system: Escherichia coli

Quick links

Citations

16 review citations

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

3 mentions without citation

Human isoprenoid synthase enzymes as therapeutic targets.
Park et al. (2014)
2 more