3WI6

Crystal structure of MAPKAP Kinase-2 (MK2) in complex with non-selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 
    0.283 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YRZClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Structure of the beta-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090

Fujino, A.Fukushima, K.Kubota, T.Matsumoto, Y.Takimoto-Kamimura, M.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1344-1348

  • DOI: https://doi.org/10.1107/S1744309113030534
  • Primary Citation of Related Structures:  
    3WI6

  • PubMed Abstract: 

    Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2), a serine/threonine kinase from the p38 mitogen-activated protein kinase signalling pathway, plays an important role in the production of TNF-α and other cytokines. In a previous report, it was shown that MK2 in complex with the selective inhibitor TEI-I01800 adopts an α-helical glycine-rich loop that is induced by the stable nonplanar conformer of TEI-I01800. To understand the mechanism of the structural change, the structure of MK2 bound to TEI-L03090, which lacks the key substituent found in TEI-I01800, was determined. MK2-TEI-L03090 has a β-sheet glycine-rich loop in common with other kinases, as predicted. This result suggests that a small compound can induce a drastic conformational change in the target protein structure and can be used to design potent and selective inhibitors.


  • Organizational Affiliation

    Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2
A, B, C, D, E
324Homo 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
GTEx:  ENSG00000162889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free:  0.283 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.061α = 90
b = 179.684β = 90
c = 254.101γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YRZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description