Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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Lattice stabilization and enhanced diffraction in human p38 alpha crystals by protein engineering.

Patel, S.B.Cameron, P.M.Frantz-Wattley, B.O'Neill, E.Becker, J.W.Scapin, G.

(2004) Biochim Biophys Acta 1696: 67-73

  • DOI: https://doi.org/10.1016/j.bbapap.2003.09.009
  • Primary Citation of Related Structures:  
    1R39, 1R3C

  • PubMed Abstract: 

    Mitogen-activated protein (MAP) kinase p38 alpha is activated in response to environmental stress and cytokines, and plays a significant role in inflammatory responses. For these reasons, it is an important target for the treatment of a wide range of inflammatory and autoimmune diseases. The crystals of p38 alpha that we obtained by published procedures were usually small, quite mosaic, and difficult to reproduce and thus posed a difficulty for the intensive high-resolution studies required for a structure-guided drug discovery approach. Based on crystallographic and biochemical evidences, we prepared a single point mutation of a surface cysteine (C162S) and found that it prevents aggregation and improves the homogeneity and stability of the enzyme. This mutation also facilitates the crystallization process and increases the diffracting power of p38 alpha crystals. Surprisingly, we found that the mutation induces a change in the conformation of a nearby surface loop resulting in stronger lattice interactions, consistent with the improved crystal quality. The mutant protein, because of its improved stability and strengthened lattice interactions, thus provides a significantly improved reagent for use in structure-based drug design for this important disease target.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratory, PO Box 2000 RY50-105, Rahway, NJ 07065, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo sapiensMutation(s): 1 
Gene Names: MAPK14
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.162α = 90
b = 84.799β = 90
c = 124.908γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description