4WTV

Crystal structure of the phosphatidylinositol 4-kinase IIbeta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The high-resolution crystal structure of phosphatidylinositol 4-kinase II beta and the crystal structure of phosphatidylinositol 4-kinase II alpha containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design.

Klima, M.Baumlova, A.Chalupska, D.Hrebabecky, H.Dejmek, M.Nencka, R.Boura, E.

(2015) Acta Crystallogr.,Sect.D 71: 1555-1563

  • DOI: 10.1107/S1399004715009505
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphatidylinositol 4-phosphate (PI4P) is the most abundant monophosphoinositide in eukaryotic cells. Humans have four phosphatidylinositol 4-kinases (PI4Ks) that synthesize PI4P, among which are PI4K IIβ and PI4K IIα. In this study, two crystal str ...

    Phosphatidylinositol 4-phosphate (PI4P) is the most abundant monophosphoinositide in eukaryotic cells. Humans have four phosphatidylinositol 4-kinases (PI4Ks) that synthesize PI4P, among which are PI4K IIβ and PI4K IIα. In this study, two crystal structures are presented: the structure of human PI4K IIβ and the structure of PI4K IIα containing a nucleoside analogue. The former, a complex with ATP, is the first high-resolution (1.9 Å) structure of a PI4K. These structures reveal new details such as high conformational heterogeneity of the lateral hydrophobic pocket of the C-lobe and together provide a structural basis for isoform-specific inhibitor design.


    Organizational Affiliation

    Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
A, B
514Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 0 
Gene Names: PI4K2B, E
EC: 2.7.1.67 3.2.1.17
Find proteins for Q8TCG2 (Homo sapiens)
Go to Gene View: PI4K2B
Go to UniProtKB:  Q8TCG2
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.010α = 90.00
b = 106.010β = 90.00
c = 214.530γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MarieCurieCzech RepublicFP7-PEOPLE-2012-CIG, project number 333916

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references