1TZD

CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the catalytic core of inositol 1,4,5-trisphosphate 3-kinase

Miller, G.J.Hurley, J.H.

(2004) Mol.Cell 15: 703-711

  • DOI: 10.1016/j.molcel.2004.08.005

  • PubMed Abstract: 
  • Soluble inositol polyphosphates are ubiquitous second messengers in eukaryotes, and their levels are regulated by an array of specialized kinases. The structure of an archetypal member of this class, inositol 1,4,5-trisphosphate 3-kinase (IP3K), has ...

    Soluble inositol polyphosphates are ubiquitous second messengers in eukaryotes, and their levels are regulated by an array of specialized kinases. The structure of an archetypal member of this class, inositol 1,4,5-trisphosphate 3-kinase (IP3K), has been determined at 2.2 angstroms resolution in complex with magnesium and adenosine diphosphate. IP3K contains a catalytic domain that is a variant of the protein kinase superfamily, and a novel four-helix substrate binding domain. The two domains are in an open conformation with respect to each other, suggesting that substrate recognition and catalysis by IP3K involves a dynamic conformational cycle. The unique helical domain of IP3K blocks access to the active site by membrane-bound phosphoinositides, explaining the structural basis for soluble inositol polyphosphate specificity.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol-trisphosphate 3-kinase A
A, B
275Rattus norvegicusMutation(s): 2 
Gene Names: Itpka
EC: 2.7.1.127
Find proteins for P17105 (Rattus norvegicus)
Go to UniProtKB:  P17105
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 71.679α = 90.00
b = 98.535β = 90.00
c = 188.745γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2013-06-19
    Type: Refinement description