3EGU

Crystal structure of the N114A mutant of ABL-SH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.

Palencia, A.Camara-Artigas, A.Pisabarro, M.T.Martinez, J.C.Luque, I.

(2010) J.Biol.Chem. 285: 2823-2833

  • DOI: 10.1074/jbc.M109.048033
  • Primary Citation of Related Structures:  
  • Also Cited By: 4JJD, 4JJC, 4JJB, 4J9I, 4J9H, 4J9G, 4J9F, 4J9E, 4J9D, 4J9C, 4J9B

  • PubMed Abstract: 
  • The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We ...

    The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.


    Related Citations: 
    • Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand
      Camara-Artigas, A.,Palencia, A.,Martinez, J.C.,Luque, I.,Gavira, J.A.,Garcia-Ruiz, J.M.
      (2007) Acta Crystallogr.,Sect.D 63: 646


    Organizational Affiliation

    Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase ABL1
A
63Homo sapiensMutation(s): 1 
Gene Names: ABL1 (ABL, JTK7)
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to Gene View: ABL1
Go to UniProtKB:  P00519
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 51.350α = 90.00
b = 51.350β = 90.00
c = 46.386γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SAINTdata scaling
SCALAdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
MOLREPphasing
SCALEPACKdata scaling
PROTEUM PLUSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-09-11 
  • Released Date: 2009-09-15 
  • Deposition Author(s): Camara-Artigas, A.

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description