› 3t9e

X-ray diffraction
1.9Å resolution

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP, 5-(PP)-IP5 (5-IP7) and MgF3 (transition state mimic)

Released:
DOI: 10.2210/pdb3t9e/pdb
PDB entry 3t9e coloured by chain, front view.
PDB entry 3t9e coloured by chain, side view.
PDB entry 3t9e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding.
Wang H, Falck JR, Hall TM, Shears SB
Nat Chem Biol 8 111-6 (2011)
PMID: 22119861

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-128893 (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

4 bound ligands:
Ligand ADP 1 x ADP
Ligand I7P 1 x I7P
Ligand MG 5 x MG
Ligand MGF 1 x MGF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 89.07Å b: 109.987Å c: 41.338Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.173 0.213
Expression system: Escherichia coli

Quick links

Citations

21 review citations

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

3 mentions without citation

The enzymes of human diphosphoinositol polyphosphate metabolism.
Thomas et al. (2014)
2 more