2O88

Crystal structure of the N114A mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Literature

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 D Biol Crystallogr 63: 646-652

  • DOI: 10.1107/S0907444907011109
  • Primary Citation of Related Structures:  
    2O88

  • PubMed Abstract: 

    • The recognition of proline-rich ligands by SH3 domains is part of the process leading to diseases such as cancer or AIDS. Understanding the molecular determinants of the binding affinity and specificity of these interactions is crucial for the development of potent inhibitors with therapeutic potential ...

    The recognition of proline-rich ligands by SH3 domains is part of the process leading to diseases such as cancer or AIDS. Understanding the molecular determinants of the binding affinity and specificity of these interactions is crucial for the development of potent inhibitors with therapeutic potential. In this study, the crystallographic structure of the N114A mutant of the SH3 domain of the Abelson leukaemia virus tyrosine kinase complexed with a high-affinity peptide is presented. The crystallization was carried out using the capillary counter-diffusion technique, which facilitates the screening, manipulation and transport of the crystals and allows the collection of X-ray data directly from the capillary in which the crystals were grown. The crystals of the N114A mutant belong to the orthorhombic P2(1)2(1)2(1) space group, with unit-cell parameters a = 48.2, b = 50.1, c = 56.4 A. The quality of the diffraction data set has allowed the structure of the complex to be determined at a resolution limit of 1.75 A.

    Organizational Affiliation: 

    Departamento de Química Física, Bioquímica y Química Inorgánica, Universidad de Almería, 04120 Almería, Spain.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase ABL1A, B58Homo sapiensMutation(s): 1 
Gene Names: ABL1, ABL, JTK7
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
PHAROS:  P00519
GTEx:  ENSG00000097007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P41 peptideC, D11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.17α = 90
b = 50.093β = 90
c = 56.431γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-12-12 
  • Released Date: 2007-05-01 
    • Deposition Author(s): Camara-Artigas, A.

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy