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: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
A
330Homo sapiensMutation(s): 0 
Gene Names: PPIP5K2 (HISPPD1, KIAA0433, VIP2)
EC: 2.7.4.21, 2.7.4.24
Find proteins for O43314 (Homo sapiens)
Go to Gene View: PPIP5K2
Go to UniProtKB:  O43314
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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

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

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
4WZ
Query on 4WZ

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.567α = 90.00
b = 110.400β = 90.00
c = 41.455γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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