4J9D Transferase Unknown Function date Feb 16, 2013
title Crystal Structure Of The N114a Mutant Of The Abl-Sh3 Domain With The High Affinity Peptide P0
authors A.Camara-Artigas
compound source
Molecule: Tyrosine-Protein Kinase Abl1
Chain: A, C, E
Fragment: Sh3 Domain (Unp Residues 60-121)
Synonym: Abelson Murine Leukemia Viral Oncogene Homolog 1, Tyrosine-Protein Kinase 1, Proto-Oncogene C-Abl, P150;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Abl, Abl1, Jtk7
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: P0
Chain: B, D, F
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Has Been Optimized To Increase Affinity
symmetry Space Group: P 32 2 1
R_factor 0.143 R_Free 0.183
length a length b length c angle alpha angle beta angle gamma
86.380 86.380 44.950 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.50 Å
ligand ACE, SO4 enzyme Transferase E.C. BRENDA
A, C, E

Primary referenceRole of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl., Palencia A, Camara-Artigas A, Pisabarro MT, Martinez JC, Luque I, J Biol Chem. 2010 Jan 22;285(4):2823-33. Epub 2009 Nov 10. PMID:19906645
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (4j9d.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (4j9d.pdb2.gz) 34 Kb
  • Biological Unit Coordinates (4j9d.pdb3.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 4J9D
  • CSU: Contacts of Structural Units for 4J9D
  • Structure Factors (209 Kb)
  • Retrieve 4J9D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4J9D from S2C, [Save to disk]
  • Re-refined 4j9d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4J9D in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4J9D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4J9D, from MSDmotif at EBI
  • Fold representative 4j9d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4j9d] [4j9d_B] [4j9d_A] [4j9d_C] [4j9d_E] [4j9d_D] [4j9d_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4J9D: [SH3 ] by SMART
  • Other resources with information on 4J9D
  • Community annotation for 4J9D at PDBWiki (http://pdbwiki.org)

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