› 3x06

X-ray diffraction
2.65Å resolution

Crystal structure of PIP4KIIBETA T201M complex with GMP

Released:
DOI: 10.2210/pdb3x06/pdb
PDB entry 3x06 coloured by chain, front view.
PDB entry 3x06 coloured by chain, side view.
PDB entry 3x06 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis.
Sumita K, Lo YH, Takeuchi K, Senda M, Kofuji S, Ikeda Y, Terakawa J, Sasaki M, Yoshino H, Majd N, Zheng Y, Kahoud ER, Yokota T, Emerling BM, Asara JM, Ishida T, Locasale JW, Daikoku T, Anastasiou D, Senda T, Sasaki AT
Mol Cell 61 187-98 (2016)
PMID: 26774281

Function and Biology Details

Reaction catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol 5-phosphate = ADP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160254 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 393 amino acids
Theoretical weight: 44.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P78356 (Residues: 31-416; Coverage: 93%)
Gene names: PIP4K2B, PIP5K2B
Sequence domains: Phosphatidylinositol-4-phosphate 5-Kinase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 5GP 5 x 5GP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: C2221
Unit cell:
a: 108.825Å b: 182.878Å c: 106.657Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.212 0.261
Expression system: Escherichia coli

Quick links

Citations

13 review citations

The Hidden Conundrum of Phosphoinositide Signaling in Cancer.
Thapa et al. (2016)
12 more

2 mentions without citation

Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study.
Ware et al. (2021)
1 more