3ZFY Transferase date Dec 12, 2012
title Crystal Structure Of Ephb3
authors J.E.Debreczeni, R.Overman, C.Truman, M.Mcalister, T.K.Attwood
compound source
Molecule: Ephrin Type-B Receptor 3
Chain: A, B
Fragment: Kinase Domain, Residues 616-910
Synonym: Eph-Like Tyrosine Kinase 2, Eph-Like Kinase 2, Emb Kinase 2, Ek2, Hek2, Tyrosine-Protein Kinase Tyro6, Ephb3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Star
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1
R_factor 0.22406 R_Free 0.25188
length a length b length c angle alpha angle beta angle gamma
46.990 56.488 61.354 93.02 90.65 90.03
method X-Ray Diffractionresolution 2.20 Å
enzyme Transferase E.C. BRENDA
A, B

Primary referenceCompleting the structural family portrait of the human EphB tyrosine kinase domains., Overman RC, Debreczeni JE, Truman CM, McAlister MS, Attwood TK, Protein Sci. 2014 Feb 15. doi: 10.1002/pro.2445. PMID:24677421
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (3zfy.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (3zfy.pdb2.gz) 85 Kb
  • CSU: Contacts of Structural Units for 3ZFY
  • Structure Factors (443 Kb)
  • Retrieve 3ZFY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZFY from S2C, [Save to disk]
  • Re-refined 3zfy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZFY 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 3ZFY
  • 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 3ZFY, from MSDmotif at EBI
  • Fold representative 3zfy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zfy] [3zfy_B] [3zfy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ZFY: [TyrKc ] by SMART
  • Other resources with information on 3ZFY
  • Community annotation for 3ZFY at PDBWiki (http://pdbwiki.org)

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