› 2i6k

X-ray diffraction
2Å resolution

Crystal structure of human type I IPP isomerase complexed with a substrate analog

Released:
DOI: 10.2210/pdb2i6k/pdb
PDB entry 2i6k coloured by chain, front view.
PDB entry 2i6k coloured by chain, side view.
PDB entry 2i6k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of human IPP isomerase: new insights into the catalytic mechanism.
Zhang C, Liu L, Xu H, Wei Z, Wang Y, Lin Y, Gong W
J Mol Biol 366 1437-46 (2007)
PMID: 17137593

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 235 amino acids
Theoretical weight: 27.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13907 (Residues: 1-227; Coverage: 100%)
Gene name: IDI1
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand MN 2 x MN
Ligand MG 4 x MG
Ligand EA2 2 x EA2
Ligand ACY 4 x ACY
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P1
Unit cell:
a: 41.363Å b: 43.074Å c: 70.466Å
α: 80.26° β: 89.98° γ: 67.95°
R-values:
R R work R free
0.222 0.22 0.262
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Mechanistic aspects of carotenoid biosynthesis.
Moise et al. (2014)
3 other articles

2 mentions without citation

A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III.
Karačić et al. (2017)
1 more