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 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.,Sect.D 63: 646-652

  • DOI: 10.1107/S0907444907011109
  • Also Cited By: 4J9B, 4J9C, 4J9D, 4J9E, 4J9F, 4J9G, 4J9H, 4J9I, 4JJB, 4JJC, 4JJD

  • 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 develo ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase ABL1
A, B
58Homo sapiensGene Names: ABL1 (ABL, JTK7)
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to Gene View: ABL1
Go to UniProtKB:  P00519
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P41 peptide
C, D
11N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.170α = 90.00
b = 50.093β = 90.00
c = 56.431γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
MOLREPphasing
DENZOdata reduction
SAINTdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description