PDBsum entry 3eg1

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protein ligands Protein-protein interface(s) links
Transferase/signaling protein PDB id
Jmol PyMol
Protein chains
58 a.a. *
11 a.a. *
SO4 ×2
Waters ×54
* Residue conservation analysis
PDB id:
Name: Transferase/signaling protein
Title: Crystal structure of the n114q mutant of abl-sh3 domain comp a designed high-affinity peptide ligand: implications for s interactions
Structure: Proto-oncogene tyrosine-protein kinase abl1. Chain: a, b. Fragment: sh3 domain, residues 60-121. Synonym: p150, c- abl, abelson murine leukemia viral oncoge 1. Engineered: yes. Mutation: yes. P41 peptide. Chain: c, d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Strain: pbat4. Gene: abl1, abl, jtk7. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the author states that the p41 peptide is a
1.85Å     R-factor:   0.192     R-free:   0.248
Authors: A.Camara-Artigas
Key ref: A.Palencia et al. (2010). Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. J Biol Chem, 285, 2823-2833. PubMed id: 19906645
10-Sep-08     Release date:   15-Sep-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00519  (ABL1_HUMAN) -  Tyrosine-protein kinase ABL1
1130 a.a.
58 a.a.*
Protein chains
No UniProt id for this chain
Struc: 10 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Non-specific protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
+ [protein]-L-tyrosine
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     protein tyrosine kinase activity     1 term  


J Biol Chem 285:2823-2833 (2010)
PubMed id: 19906645  
Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
A.Palencia, A.Camara-Artigas, M.T.Pisabarro, J.C.Martinez, I.Luque.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21472810 C.B.McDonald, K.L.Seldeen, B.J.Deegan, V.Bhat, and A.Farooq (2011).
Binding of the cSH3 domain of Grb2 adaptor to two distinct RXXK motifs within Gab1 docker employs differential mechanisms.
  J Mol Recognit, 24, 585-596.  
  20687233 M.Andujar-Sánchez, V.Jara-Perez, E.S.Cobos, and A.Cámara-Artigas (2011).
A thermodynamic characterization of the interaction of 8-anilino-1-naphthalenesulfonic acid with native globular proteins: the effect of the ligand dimerization in the analysis of the binding isotherms.
  J Mol Recognit, 24, 548-556.  
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