› 2pny

X-ray diffraction
1.81Å resolution

Structure of Human Isopentenyl-diphosphate Delta-isomerase 2

Released:
DOI: 10.2210/pdb2pny/pdb
PDB entry 2pny coloured by chain, front view.
PDB entry 2pny coloured by chain, side view.
PDB entry 2pny coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Walker JR, Davis T, Butler-Cole C, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon S, Structural Genomics Consortium (SGC)

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-189800 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopentenyl-diphosphate delta-isomerase 2 Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 28.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BXS1 (Residues: 1-227; Coverage: 100%)
Gene name: IDI2
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand CA 1 x CA
Ligand MN 1 x MN
Ligand POP 1 x POP
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 50.897Å b: 52.815Å c: 96.391Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.149 0.148 0.182
Expression system: Escherichia coli BL21(DE3)

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