4HVW

Crystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity peptide VSL12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II.

Bacarizo, J.Camara-Artigas, A.

(2013) Acta Crystallogr.,Sect.D 69: 756-766

  • DOI: 10.1107/S0907444913001522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The atomic resolution crystal structures of complexes between the SH3 domain of the c-Src tyrosine kinase and two high-affinity peptides belonging to class I and class II have been solved. The crystals of the Thr98Asp and Thr98Glu mutants in complex ...

    The atomic resolution crystal structures of complexes between the SH3 domain of the c-Src tyrosine kinase and two high-affinity peptides belonging to class I and class II have been solved. The crystals of the Thr98Asp and Thr98Glu mutants in complex with the APP12 peptide (APPLPPRNRPRL) belonged to the trigonal space group P3121 and in both cases the asymmetric unit was composed of one molecule of the SH3-APP12 complex. The crystals of the Thr98Glu mutant in complex with the VSL12 peptide (VSLARRPLPLP) belonged to the trigonal space group P3221 and the asymmetric unit was also composed of a single molecule of the SH3-VSL12 complex. All crystals were obtained in the presence of PEG 300 under the same conditions as reported for the intertwined dimeric structure of the c-Src SH3 domain, but the presence of the peptide stabilizes the monomeric form of the domain. These structures allow a detailed analysis of the role of salt bridges, cation-π interactions and hydrogen bonds in the binding of proline-rich motifs to the c-Src SH3 domain. Moreover, these crystallographic structures allow the role of water molecules in the binding of these motifs to the c-Src SH3 domain to be studied for the first time.


    Organizational Affiliation

    Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence, Carretera de Sacramento, 04120 Almería, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A
61Gallus gallusMutation(s): 2 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Go to Gene View: SRC
Go to UniProtKB:  P00523
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SYNTHETIC PEPTIDE Acetyl-VSLARRPLPPLP
B
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.134 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 37.442α = 90.00
b = 37.442β = 90.00
c = 85.624γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
ADSCdata collection
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-07 
  • Released Date: 2013-05-01 
  • Deposition Author(s): Camara-Artigas, A.

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references