› 3udz

X-ray diffraction
2.5Å resolution

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.

Released:
DOI: 10.2210/pdb3udz/pdb
PDB entry 3udz coloured by chain, front view.
PDB entry 3udz coloured by chain, side view.
PDB entry 3udz coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Inositol phosphate-induced stabilization of inositol 1,3,4,5,6-pentakisphosphate 2-kinase and its role in substrate specificity.
Gosein V, Leung TF, Krajden O, Miller GJ
Protein Sci 21 737-42 (2012)
PMID: 22362712

Function and Biology Details

Reaction catalysed: 
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol hexakisphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188160 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Inositol-pentakisphosphate 2-kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 493 amino acids
Theoretical weight: 55.75 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q93YN9 (Residues: 1-451; Coverage: 100%)
Gene names: At5g42810, IPK1, MJB21.19
Sequence domains: Inositol-pentakisphosphate 2-kinase
Structure domains: Inositol-pentakisphosphate 2-kinase, N-lobe

Ligands and Environments

4 bound ligands:
Ligand IHP 2 x IHP
Ligand ADP 2 x ADP
Ligand MG 4 x MG
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 59.057Å b: 59.394Å c: 82.755Å
α: 89.84° β: 82.58° γ: 63.36°
R-values:
R R work R free
0.192 0.189 0.26
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

Inositol Phosphates and Retroviral Assembly: A Cellular Perspective.
Ricaña et al. (2021)
6 other articles

3 mentions without citation

Inositol phosphate-induced stabilization of inositol 1,3,4,5,6-pentakisphosphate 2-kinase and its role in substrate specificity.
Gosein et al. (2012)
2 more