2JBP

Protein kinase MK2 in complex with an inhibitor (crystal form-2, co- crystallization)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.215 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for a high affinity inhibitor bound to protein kinase MK2.

Hillig, R.C., Eberspaecher, U., Monteclaro, F., Huber, M., Nguyen, D., Mengel, A., Muller-Tiemann, B., Egner, U.

(2007) J Mol Biol 369: 735-745

  • DOI: https://doi.org/10.1016/j.jmb.2007.03.004
  • Primary Citation of Related Structures:  
    2JBO, 2JBP

  • PubMed Abstract: 

    • The Ser/Thr protein kinase MAPKAP kinase 2 (MK2) plays a crucial role in inflammation. We determined the structure of the kinase domain of MK2 in complex with a low molecular mass inhibitor in two different crystal forms, obtained from soaking and co-crystallization ...

    The Ser/Thr protein kinase MAPKAP kinase 2 (MK2) plays a crucial role in inflammation. We determined the structure of the kinase domain of MK2 in complex with a low molecular mass inhibitor in two different crystal forms, obtained from soaking and co-crystallization. To our knowledge, these are the first structures of MK2 showing the binding mode of an inhibitor with high binding affinity (IC50 8.5 nM). The two crystal forms revealed conformational flexibility in the binding site and extend the experimental basis for rational drug design. Crystal form-1 contained one MK2 molecule per asymmetric unit. Form-2 contained 12 molecules, which arrange into two different types of MK2 trimers. One of them may serve as a model for an intermediate state during substrate phosphorylation, as each MK2 monomer places its activation segment into the substrate peptide binding groove of the trimer neighbor.

    Related Citations: 
    • Identifying Protein Construct Variants with Increased Crystallization Propensity-A Case Study.
      Malawski, G.A., Hillig, R.C., Monteclaro, F., Eberspaecher, U., Schmitz, A.A., Crusius, K., Huber, M., Egner, U., Donner, P., Muller-Tiemann, B.
      (2006) Protein Sci 15: 2718
    Organizational Affiliation: 

    Bayer Schering Pharma AG, Research Laboratories, D-13342 Berlin, Germany. roman.hillig@schering.de



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAP KINASE-ACTIVATED PROTEIN KINASE 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
326Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49137 (Homo sapiens)
Explore P49137 
Go to UniProtKB:  P49137
PHAROS:  P49137
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
P4O PDBBind:  2JBP IC50: 8.5 (nM) from 1 assay(s)
BindingDB:  2JBP IC50: 8.5 (nM) from 1 assay(s)
EC50: 49 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.983α = 90
b = 215.564β = 90
c = 179.9γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
BEASTphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-16
    Changes: Data collection, Database references, Derived calculations