› 2ybx

X-ray diffraction
2.56Å resolution

Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha

Released:
DOI: 10.2210/pdb2ybx/pdb
Model geometry
Fit model/data
PDB entry 2ybx coloured by chain, front view.
PDB entry 2ybx coloured by chain, side view.
PDB entry 2ybx coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tresaugues L, Moche M, Arrowsmith CH, Berglund H, Bountra C, Collins R, Edwards AM, Ekblad T, Flodin S, Graslund S, Karlberg T, Kotenyova T, Kouznetsova E, Nyman T, Persson C, Schuler H, Siponen MI, Thorsell AG, Wahlberg E, Weigelt J, Nordlund P

Function and Biology Details

Reaction catalysed: 
a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + ATP =a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) +ADP + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155728 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 394 amino acids
Theoretical weight: 45.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P48426 (Residues: 35-405; Coverage: 91%)
  • Best match: P48426-2 (Residues: 1-346)
Gene names: PI5P4KA, PIP4K2A, PIP5K2, PIP5K2A
Sequence domains: Phosphatidylinositol-4-phosphate 5-Kinase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand PO4 1 x PO4
1 modified residue:
Ligand PHD 2 x PHD

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 44.04Å b: 98.508Å c: 104.879Å
α: 90° β: 93.43° γ: 90°
R-values:
R R work R free
0.191 0.188 0.238
Expression system: Escherichia coli BL21(DE3)

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