Crystal Structure of Inhibitor of kappaB kinase beta (I4122)

Experimental Data Snapshot

  • Resolution: 4.00 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.273 

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Crystal structure of inhibitor of KappaB kinase Beta.

Xu, G.Lo, Y.C.Li, Q.Napolitano, G.Wu, X.Jiang, X.Dreano, M.Karin, M.Wu, H.

(2011) Nature 472: 325-330

  • DOI: https://doi.org/10.1038/nature09853
  • Primary Citation of Related Structures:  
    3QA8, 3RZF

  • PubMed Abstract: 

    Inhibitor of κB (IκB) kinase (IKK) phosphorylates IκB proteins, leading to their degradation and the liberation of nuclear factor κB for gene transcription. Here we report the crystal structure of IKKβ in complex with an inhibitor, at a resolution of 3.6 Å. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, α-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix-loop-helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with IκBα that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKKβ dimerization, but dimerization per se is not important for maintaining IKKβ activity and instead is required for IKKβ activation. Other IKK family members, IKKα, TBK1 and IKK-i, may have a similar trimodular architecture and function.

  • Organizational Affiliation

    Department of Biochemistry, Weill Cornell Medical College, New York, New York 10021, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MGC80376 protein677Xenopus laevisMutation(s): 2 
Gene Names: ikbkb.Likbkbikk-betaikk2ikkbikkbetaMGC80376
Find proteins for Q6INT1 (Xenopus laevis)
Explore Q6INT1 
Go to UniProtKB:  Q6INT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6INT1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on XNM

Download Ideal Coordinates CCD File 
B [auth A](4-{[4-(4-chlorophenyl)pyrimidin-2-yl]amino}phenyl)[4-(2-hydroxyethyl)piperazin-1-yl]methanone
C23 H24 Cl N5 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 4.00 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.273 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.656α = 90
b = 164.656β = 90
c = 273.458γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance