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 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.jmb.2007.03.004
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAP KINASE-ACTIVATED PROTEIN KINASE 2
A, B, C, D, E, F, G, H, I, J, K, L
326Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK2
EC: 2.7.11.1
Find proteins for P49137 (Homo sapiens)
Go to Gene View: MAPKAPK2
Go to UniProtKB:  P49137
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4O
Query on P4O

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, K, L
2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE
C21 H16 N4 O
OWFLADWRSCINST-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P4OIC50: 8.5 nM (100) BINDINGDB
P4OEC50: 49 nM (100) BINDINGDB
P4OIC50: 8.5 nM PDBBIND
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 = 90.00
b = 215.564β = 90.00
c = 179.900γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
BEASTphasing
CNXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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