› 6fl3

X-ray diffraction
2.36Å resolution

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

Released:
DOI: 10.2210/pdb6fl3/pdb
PDB entry 6fl3 coloured by chain, front view.
PDB entry 6fl3 coloured by chain, side view.
PDB entry 6fl3 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase.
Whitfield H, Gilmartin M, Baker K, Riley AM, Godage HY, Potter BVL, Hemmings AM, Brearley CA
J Med Chem 61 8838-8846 (2018)
PMID: 30160967

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: 470 amino acids
Theoretical weight: 52.86 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93YN9 (Residues: 1-451; Coverage: 100%)
Gene names: At5g42810, IPK1, MJB21.19
Sequence domains: Inositol-pentakisphosphate 2-kinase

Ligands and Environments

5 bound ligands:
Ligand 5MY 2 x 5MY
Ligand ADP 2 x ADP
Ligand MG 4 x MG
Ligand ZN 2 x ZN
Ligand B3P 2 x B3P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 58.95Å b: 59.01Å c: 83.36Å
α: 88.98° β: 89.56° γ: 63.65°
R-values:
R R work R free
0.158 0.154 0.217
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Suramin and NF449 are IP5K inhibitors that disrupt inositol hexakisphosphate-mediated regulation of cullin-RING ligase and sensitize cancer cells to MLN4924/pevonedistat.
Zhang et al. (2020)
3 more