Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.06 kDa 
• Atom Count: 546 
• Modelled Residue Count: 63 
• Deposited Residue Count: 63 
• Unique protein chains: 1

3EG3

Crystal structure of the N114A mutant of ABL-SH3 domain

• DOI: 10.2210/pdb3EG3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-09-10 Released: 2009-09-15 
• Deposition Author(s): Camara-Artigas, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.

Palencia, A., Camara-Artigas, A., Pisabarro, M.T., Martinez, J.C., Luque, I.

(2010) J Biol Chem 285: 2823-2833

• PubMed: 19906645 
• DOI: 10.1074/jbc.M109.048033
• Primary Citation of Related Structures:  
  3EG0, 3EG1, 3EG2, 3EG3, 3EGU


• PubMed Abstract: 
  

The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase ABL1	A	63	Homo sapiens	Mutation(s): 1  Gene Names: ABL1, ABL, JTK7 EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens) Explore P00519  Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS:  P00519 GTEx:  ENSG00000097007

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.819	α = 90
b = 53.096	β = 90
c = 41.296	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-10 
• Released Date: 2009-09-15 
Deposition Author(s): Camara-Artigas, A.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance