1NZV

Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYIpYVPA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural and Thermodynamic Basis for the Interaction of the Src SH2 domain with the Activated form of the PDGF beta-receptor

Lubman, O.Y., Waksman, G.

(2003) J.Mol.Biol. 328: 655-668

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Recruitment of the Src kinase to the activated form of the platelet-derived growth factor (PDGF) receptor involves recognition of a unique sequence motif in the juxtamembrane region of the receptor by the Src homology 2 (SH2) domain of the enzyme. Th ...

    Recruitment of the Src kinase to the activated form of the platelet-derived growth factor (PDGF) receptor involves recognition of a unique sequence motif in the juxtamembrane region of the receptor by the Src homology 2 (SH2) domain of the enzyme. This motif contains two phosphotyrosine residues separated by one residue (sequence pYIpYV where pY indicates a phosphotyrosine). Here, we provide the thermodynamic and structural basis for the binding of this motif by the Src SH2 domain. We show that the second phosphorylation event increases the free energy window for specific interaction and that the physiological target is exquisitely designed for the task of recruiting specifically an SH2 domain which otherwise demonstrates very little intrinsic ability to discriminate sequences C-terminal to the first phosphorylation event. Surprisingly, we show that water plays a role in the recognition process.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase transforming protein SRC
A, B
103Avian leukosis virus RSAMutation(s): 0 
Gene Names: V-SRC
EC: 2.7.10.2
Find proteins for P00524 (Avian leukosis virus RSA)
Go to UniProtKB:  P00524
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Doubly phosphorylated peptide PQpYIpYVPA
C
8N/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
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4
Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PTRΔG: -21.4 kJ/mol (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.256α = 90.00
b = 67.727β = 90.00
c = 29.636γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-04-30
    Type: Data collection