› 5e3u

X-ray diffraction
3.6Å resolution

Crystal structure of phosphatidylinositol-4-phosphate 5-kinase

Released:
DOI: 10.2210/pdb5e3u/pdb
PDB entry 5e3u coloured by chain, front view.
PDB entry 5e3u coloured by chain, side view.
PDB entry 5e3u coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Mechanism of substrate specificity of phosphatidylinositol phosphate kinases.
Muftuoglu Y, Xue Y, Gao X, Wu D, Ha Y
Proc Natl Acad Sci U S A 113 8711-6 (2016)
PMID: 27439870

Function and Biology Details

Reaction catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol 4-phosphate = ADP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175873 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PIPK domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 372 amino acids
Theoretical weight: 42.26 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q503I3 (Residues: 56-427; Coverage: 67%)
Gene names: pip5k1a, pip5k1aa, zgc:110576
Sequence domains: Phosphatidylinositol-4-phosphate 5-Kinase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ANP 1 x ANP
Ligand MN 2 x MN
Ligand SE4 2 x SE4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43212
Unit cell:
a: 88.134Å b: 88.134Å c: 155.757Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.201 0.261
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Lipid composition of the cancer cell membrane.
Szlasa et al. (2020)
4 more

2 mentions without citation

Mechanism of substrate specificity of phosphatidylinositol phosphate kinases.
Muftuoglu et al. (2016)
1 more