3U9C

Structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit with the ATP-competitive inhibitor resorufin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias.

Klopffleisch, K.Issinger, O.G.Niefind, K.

(2012) Acta Crystallogr.,Sect.D 68: 883-892

  • DOI: 10.1107/S0907444912016587
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A low-resolution structure of the catalytic subunit CK2α of human protein kinase CK2 (formerly known as casein kinase 2) in complex with the ATP-competitive inhibitor resorufin is presented. The structure supplements previous human CK2α structures in ...

    A low-resolution structure of the catalytic subunit CK2α of human protein kinase CK2 (formerly known as casein kinase 2) in complex with the ATP-competitive inhibitor resorufin is presented. The structure supplements previous human CK2α structures in which the interdomain hinge/helix αD region adopts a closed conformation correlating to a canonically established catalytic spine as is typical for eukaryotic protein kinases. In the corresponding crystal packing the hinge/helix αD region is nearly unaffected by crystal contacts, so that largely unbiased conformational adaptions are possible. This is documented by published human CK2α structures with the same crystal packing but with an open hinge/helix αD region, one of which has been redetermined here with a higher symmetry. An overview of all published human CK2α crystal packings serves as the basis for a discussion of the factors that determine whether the open or the closed hinge/helix αD conformation is adopted. Lyotropic salts in crystallization support the closed conformation, in which the Phe121 side chain complements the hydrophobic catalytic spine ensemble. Consequently, genuine ligand effects on the hinge/helix αD conformation can be best studied under moderate salt conditions. Ligands that stabilize either the open or the closed conformation by hydrogen bonds are known, but a general rule is not yet apparent.


    Related Citations: 
    • Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
      Yde, C.W.,Ermakova, I.,Issinger, O.G.,Niefind, K.
      (2005) J.Mol.Biol. 347: 399
    • The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules.
      Raaf, J.,Brunstein, E.,Issinger, O.G.,Niefind, K.
      (2008) Chem.Biol. 15: 111
    • Conformational plasticity of the catalytic subunit of protein kinase CK2 and its consequences for regulation and drug design.
      Niefind, K.,Issinger, O.G.
      (2010) Biochim.Biophys.Acta 1804: 484
    • Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights.
      Niefind, K.,Raaf, J.,Issinger, O.G.
      (2009) Cell.Mol.Life Sci. 66: 1800


    Organizational Affiliation

    Department für Chemie, Institut für Biochemie, Universität zu Köln, Otto-Fischer-Strasse 12-14, D-50674 Köln, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A, B
335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
04G
Query on 04G

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Download CCD File 
A, B
7-hydroxy-3H-phenoxazin-3-one
RESORUFIN
C12 H7 N O3
HSSLDCABUXLXKM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
04GKi: 1300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.777α = 90.00
b = 127.777β = 90.00
c = 125.766γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references