› 1ppv

X-ray diffraction
1.7Å resolution

ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE IN COMPLEX WITH THE BROMOHYDRINE OF IPP

Released:
DOI: 10.2210/pdb1ppv/pdb
PDB entry 1ppv coloured by chain, front view.
PDB entry 1ppv coloured by chain, side view.
PDB entry 1ppv coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A crystallographic investigation of phosphoantigen binding to isopentenyl pyrophosphate/dimethylallyl pyrophosphate isomerase.
Wouters J, Yin F, Song Y, Zhang Y, Oudjama Y, Stalon V, Droogmans L, Morita CT, Oldfield E
J Am Chem Soc 127 536-7 (2005)
PMID: 15643873

Function and Biology Details

Reaction catalysed: 
Isopentenyl diphosphate = prenyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175139 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopentenyl-diphosphate Delta-isomerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 183 amino acids
Theoretical weight: 20.64 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46822 (Residues: 1-182; Coverage: 100%)
Gene names: JW2857, b2889, idi, ygfV
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

3 bound ligands:
Ligand MN 2 x MN
Ligand MG 2 x MG
Ligand BHI 2 x BHI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P212121
Unit cell:
a: 69.147Å b: 71.821Å c: 92.019Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.188 0.243
Expression system: Escherichia coli

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Citations

1 review citation

Neuro(active)steroids actions at the neuromodulatory sigma1 (sigma1) receptor: biochemical and physiological evidences, consequences in neuroprotection.
Maurice et al. (2006)
4 other articles

1 mention without citation

The evolution of function within the Nudix homology clan.
Srouji et al. (2017)