› 6cn2

X-ray diffraction
3.1Å resolution

Crystal structure of zebrafish Phosphatidylinositol-4-phosphate 5- kinase alpha isoform D236N with bound ATP/Ca2+

Released:
DOI: 10.2210/pdb6cn2/pdb
PDB entry 6cn2 coloured by chain, front view.
PDB entry 6cn2 coloured by chain, side view.
PDB entry 6cn2 coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5Kγ.
Zeng X, Uyar A, Sui D, Donyapour N, Wu D, Dickson A, Hu J
Biochem J 475 2257-2269 (2018)
PMID: 29959184

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: 394 amino acids
Theoretical weight: 44.87 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q503I3 (Residues: 49-431; Coverage: 69%)
Gene names: pip5k1a, pip5k1aa, zgc:110576
Sequence domains: Phosphatidylinositol-4-phosphate 5-Kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P43212
Unit cell:
a: 89.036Å b: 89.036Å c: 157.783Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.226 0.259
Expression system: Escherichia coli

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Citations

2 citation in other articles

Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods.
Ginex et al. (2021)
1 more

1 mention without citation

Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5Kγ.
Zeng et al. (2018)