› 4axd

X-ray diffraction
2.05Å resolution

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with AMPPNP

Released:
DOI: 10.2210/pdb4axd/pdb
PDB entry 4axd coloured by chain, front view.
PDB entry 4axd coloured by chain, side view.
PDB entry 4axd coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Conformational changes in inositol 1,3,4,5,6-pentakisphosphate 2-kinase upon substrate binding: role of N-terminal lobe and enantiomeric substrate preference.
Baños-Sanz JI, Sanz-Aparicio J, Whitfield H, Hamilton C, Brearley CA, González B
J Biol Chem 287 29237-49 (2012)
PMID: 22745128

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

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188161 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Inositol-pentakisphosphate 2-kinase Chain: A
Molecule details ›
Chain: A
Length: 456 amino acids
Theoretical weight: 51.21 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
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 ANP 1 x ANP
Ligand ZN 1 x ZN
Ligand SO4 5 x SO4
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21212
Unit cell:
a: 100.23Å b: 71.8Å c: 63.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.194 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 citation in other articles

An ATP-responsive metabolic cassette comprised of inositol tris/tetrakisphosphate kinase 1 (ITPK1) and inositol pentakisphosphate 2-kinase (IPK1) buffers diphosphosphoinositol phosphate levels.
Whitfield et al. (2020)
7 more

1 mention without citation

Conformational changes in inositol 1,3,4,5,6-pentakisphosphate 2-kinase upon substrate binding: role of N-terminal lobe and enantiomeric substrate preference.
Baños-Sanz et al. (2012)