1F0Q

CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOR EMODIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The replacement of ATP by the competitive inhibitor emodin induces conformational modifications in the catalytic site of protein kinase CK2.

Battistutta, R., Sarno, S., De Moliner, E., Papinutto, E., Zanotti, G., Pinna, L.A.

(2000) J Biol Chem 275: 29618-29622

  • DOI: 10.1074/jbc.M004257200
  • Primary Citation of Related Structures:  
    1F0Q

  • PubMed Abstract: 

    • The structure of a complex between the catalytic subunit of Zea mays CK2 and the nucleotide binding site-directed inhibitor emodin (3-methyl-1,6,8-trihydroxyanthraquinone) was solved at 2.6-A resolution. Emodin enters the nucleotide binding site of the enzyme, filling a hydrophobic pocket between the N-terminal and the C-terminal lobes, in the proximity of the site occupied by the base rings of the natural co-substrates ...

    The structure of a complex between the catalytic subunit of Zea mays CK2 and the nucleotide binding site-directed inhibitor emodin (3-methyl-1,6,8-trihydroxyanthraquinone) was solved at 2.6-A resolution. Emodin enters the nucleotide binding site of the enzyme, filling a hydrophobic pocket between the N-terminal and the C-terminal lobes, in the proximity of the site occupied by the base rings of the natural co-substrates. The interactions between the inhibitor and CK2 alpha are mainly hydrophobic. Although the C-terminal domain of the enzyme is essentially identical to the ATP-bound form, the beta-sheet in the N-terminal domain is altered by the presence of emodin. The structural data presented here highlight the flexibility of the kinase domain structure and provide information for the design of selective ATP competitive inhibitors of protein kinase CK2.

    Related Citations: 
    • Crystal Structure of the Catalitic Subunit of Protein Kinase CK2 from Zea mays at 2.1 A Resolution
      Niefind, K., Guerra, B., Pinna, L.A., Issinger, O.G., Schomburg, D.
      (1998) EMBO J 17: 2451
    • GTP Plus Water Mimic ATP in the Active Site of Protein Kinase CK2
      Niefind, K., Putter, M., Guerra, B., Issinger, O.G., Schomburg, D.
      (1999) Nat Struct Biol 6: 1100
    Organizational Affiliation: 

    Department of Organic Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN KINASE CK2, ALPHA SUBUNIT A332Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for P28523 (Zea mays)
Explore P28523 
Go to UniProtKB:  P28523
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMO
Query on EMO
Download Ideal Coordinates CCD File 
A
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
C15 H10 O5
RHMXXJGYXNZAPX-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EMOKi:  1850   nM  BindingDB
EMOIC50 :  1000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.084α = 90
b = 52.08β = 99.33
c = 44.878γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance