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 

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
  • Also Cited By: 3FL5

  • 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 t ...

    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.Mol.Biol. 6: 1100


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN KINASE CK2, ALPHA SUBUNIT
A
332Zea maysGene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMO
Query on EMO

Download SDF File 
Download CCD File 
A
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
EMODIN
C15 H10 O5
RHMXXJGYXNZAPX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EMOKi: 1850 nM (100) 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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.084α = 90.00
b = 52.080β = 99.33
c = 44.878γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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