› 6r4v

X-ray diffraction
2.2Å resolution

Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate

Released:
DOI: 10.2210/pdb6r4v/pdb
PDB entry 6r4v coloured by chain, front view.
PDB entry 6r4v coloured by chain, side view.
PDB entry 6r4v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase-Bisphosphonate Interactions: A Crystallographic and Computational Analysis.
Lisnyansky M, Yariv E, Segal O, Marom M, Loewenstein A, Ben-Tal N, Giladi M, Haitin Y
Mol Pharmacol 96 580-588 (2019)
PMID: 31427399

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132011 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Geranylgeranyl pyrophosphate synthase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 307 amino acids
Theoretical weight: 35.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95749 (Residues: 1-300; Coverage: 100%)
Gene name: GGPS1
Sequence domains: Polyprenyl synthetase

Ligands and Environments

3 bound ligands:
Ligand MG 17 x MG
Ligand BFQ 6 x BFQ
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P212121
Unit cell:
a: 68.45Å b: 153.01Å c: 198.59Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.224
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Geranylgeranyl diphosphate synthase: Role in human health, disease and potential therapeutic target.
Muehlebach et al. (2023)
1 more

1 mention without citation

5-(Indol-2-yl)pyrazolo[3,4-b]pyridines as a New Family of TASK-3 Channel Blockers: A Pharmacophore-Based Regioselective Synthesis.
Ramírez et al. (2021)