› 3udt

X-ray diffraction
3.1Å resolution

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP5.

Released:
DOI: 10.2210/pdb3udt/pdb
PDB entry 3udt coloured by chain, front view.
PDB entry 3udt coloured by chain, side view.
PDB entry 3udt 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:
monomeric (preferred)
homo dimer
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: 55.33 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 5MY 2 x 5MY
Ligand ADP 2 x ADP
Ligand MG 2 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 59.362Å b: 59.913Å c: 83.146Å
α: 90.02° β: 97.04° γ: 116.81°
R-values:
R R work R free
0.213 0.21 0.276
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

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

1 mention 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)