› 4nzo

X-ray diffraction
1.9Å resolution

Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 2,5-DI-O-BN-INSP4

Released:
DOI: 10.2210/pdb4nzo/pdb
PDB entry 4nzo coloured by chain, front view.
PDB entry 4nzo coloured by chain, side view.
PDB entry 4nzo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthetic inositol phosphate analogs reveal that PPIP5K2 has a surface-mounted substrate capture site that is a target for drug discovery.
Wang H, Godage HY, Riley AM, Weaver JD, Shears SB, Potter BV
OpenAccess logo Chem Biol 21 689-99 (2014)
PMID: 24768307

Function and Biology Details

Reaction catalysed: 
ATP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-519995 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43314 (Residues: 41-366; Coverage: 26%)
Gene names: HISPPD1, KIAA0433, PPIP5K2, VIP2
Sequence domains: Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ANP 1 x ANP
Ligand 2OV 1 x 2OV
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 89.11Å b: 111.133Å c: 41.299Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.215
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Inositol pyrophosphates: why so many phosphates?
Shears SB. (2015)
10 more

3 mentions without citation

Picornavirus RNA Recombination Counteracts Error Catastrophe.
Kempf et al. (2019)
2 more