3FJ5

Crystal structure of the c-src-SH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Intertwined dimeric structure for the SH3 domain of the c-Src tyrosine kinase induced by polyethylene glycol binding

Morel, B.Ruiz-Sanz, J.Luque, I.

(2009) Febs Lett. 583: 749-753

  • DOI: 10.1016/j.febslet.2009.01.036

  • PubMed Abstract: 
  • Here we report the first crystal structure of the SH3 domain of the cellular Src tyrosine kinase (c-Src-SH3) domain on its own. In the crystal two molecules of c-Src-SH3 exchange their -RT loops generating an intertwined dimer, in which the two SH3 u ...

    Here we report the first crystal structure of the SH3 domain of the cellular Src tyrosine kinase (c-Src-SH3) domain on its own. In the crystal two molecules of c-Src-SH3 exchange their -RT loops generating an intertwined dimer, in which the two SH3 units, preserving the binding site configuration, are oriented to allow simultaneous binding of two ligand molecules. The dimerization of c-Src-SH3 is induced, both in the crystal and in solution, by the binding of a PEG molecule at the dimer interface, indicating that this type of conformations are energetically close to the native structure. These results have important implications respect to in vivo oligomerization and amyloid aggregation.


    Organizational Affiliation

    Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería, Carretera Sacramento s/n, 04120 Almería, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
57Gallus gallusMutation(s): 1 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Go to Gene View: SRC
Go to UniProtKB:  P00523
Small Molecules
Ligands 5 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
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.206 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 46.596α = 90.00
b = 46.596β = 90.00
c = 128.064γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-12-14 
  • Released Date: 2009-03-03 
  • Deposition Author(s): Camara-Artigas, A.

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance