› 2ick

X-ray diffraction
1.93Å resolution

Human isopentenyl diphophate isomerase complexed with substrate analog

Released:
DOI: 10.2210/pdb2ick/pdb
PDB entry 2ick coloured by chain, front view.
PDB entry 2ick coloured by chain, side view.
PDB entry 2ick coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis.
Zheng W, Sun F, Bartlam M, Li X, Li R, Rao Z
J Mol Biol 366 1447-58 (2007)
PMID: 17250851

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171834 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopentenyl-diphosphate Delta-isomerase 1 Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 26.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13907 (Residues: 1-227; Coverage: 100%)
Gene name: IDI1
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MN 1 x MN
Ligand DMA 1 x DMA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 40.812Å b: 47.396Å c: 116.817Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.205 0.255
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Mechanistic aspects of carotenoid biosynthesis.
Moise et al. (2014)
1 more

4 mentions without citation

Mechanical strength of 17,134 model proteins and cysteine slipknots.
Sikora et al. (2009)
3 more