4YC4

Crystal structure of phosphatidyl inositol 4-kinase II alpha in complex with nucleotide analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 D Biol Crystallogr 71: 1555-1563

  • DOI: 10.1107/S1399004715009505
  • Primary Citation of Related Structures:  
    4YC4, 4WTV

  • 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 structures are presented: the structure of human PI4K IIβ and the structure of PI4K IIα containing a nucleoside analogue ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha A556Homo sapiensEscherichia virus T4Mutation(s): 0 
Gene Names: PI4K2AT4Tp126
EC: 2.7.1.67 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
Find proteins for Q9BTU6 (Homo sapiens)
Explore Q9BTU6 
Go to UniProtKB:  Q9BTU6
NIH Common Fund Data Resources
PHAROS:  Q9BTU6
Find proteins for D9IEF7 (Enterobacteria phage T4)
Explore D9IEF7 
Go to UniProtKB:  D9IEF7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
M59
Query on M59

Download Ideal Coordinates CCD File 
A
[(1S,3S,4S)-3-(6-amino-9H-purin-9-yl)bicyclo[2.2.1]hept-1-yl]methanol
C13 H17 N5 O
JHMDCTCOXQJTFX-RVBZMBCESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKi:  100100   nM  BindingDB
ADPIC50:  145300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.414α = 90
b = 103.77β = 90
c = 78.109γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-19 
  • Released Date: 2015-07-15 
  • Deposition Author(s): Klima, M., Boura, E.

Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicInterBioMed LO1302

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence, Derived calculations