5BYA

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PCP)2-IP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.145 

wwPDB Validation 3D Report Full Report



Literature

Synthetic tools for studying the chemical biology of InsP8.

Riley, A.M.Wang, H.Shears, S.B.L Potter, B.V.

(2015) Chem Commun (Camb) 51: 12605-12608

  • DOI: 10.1039/c5cc05017k
  • Primary Citation of Related Structures:  
    5BYA, 5BYB

  • PubMed Abstract: 
  • To synthesise stabilised mimics of InsP8, the most phosphorylated inositol phosphate signalling molecule in Nature, we replaced its two diphosphate (PP) groups with either phosphonoacetate (PA) or methylenebisphosphonate (PCP) groups. Utility of the ...

    To synthesise stabilised mimics of InsP8, the most phosphorylated inositol phosphate signalling molecule in Nature, we replaced its two diphosphate (PP) groups with either phosphonoacetate (PA) or methylenebisphosphonate (PCP) groups. Utility of the PA and PCP analogues was verified by structural and biochemical analyses of their interactions with enzymes of InsP8 metabolism.


    Organizational Affiliation

    Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2A330Homo sapiensMutation(s): 0 
Gene Names: PPIP5K2HISPPD1KIAA0433VIP2
EC: 2.7.4.21 (PDB Primary Data), 2.7.4.24 (PDB Primary Data)
Find proteins for O43314 (Homo sapiens)
Explore O43314 
Go to UniProtKB:  O43314
NIH Common Fund Data Resources
PHAROS  O43314
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4WZ
Query on 4WZ

Download CCD File 
A
{[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)
C8 H24 O28 P8
WDYISGXURTYYJP-ZDJZFTHGSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.567α = 90
b = 110.4β = 90
c = 41.455γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-06-10 
  • Released Date: 2015-07-22 
  • Deposition Author(s): Wang, H., Shears, S.B.

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release