› 2xao

X-ray diffraction
2.9Å resolution

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

Released:
DOI: 10.2210/pdb2xao/pdb
PDB entry 2xao coloured by chain, front view.
PDB entry 2xao coloured by chain, side view.
PDB entry 2xao coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition.
González B, Baños-Sanz JI, Villate M, Brearley CA, Sanz-Aparicio J
Proc Natl Acad Sci U S A 107 9608-13 (2010)
PMID: 20453199

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:
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: 451 amino acids
Theoretical weight: 50.72 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

2 bound ligands:
Ligand 5MY 2 x 5MY
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 58.761Å b: 112.737Å c: 144.454Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.225 0.291
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

31 citation in other articles

Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding.
Wang et al. (2011)
30 more

5 mentions without citation

Current strategies for the design of PROTAC linkers: a critical review.
Troup et al. (2020)
4 more