3ZFM Transferase date Dec 12, 2012
title Crystal Structure Of Ephb2
authors J.E.Debreczeni, R.Overman, C.Truman, M.Mcalister, T.K.Attwood
compound source
Molecule: Ephrin Type-B Receptor 2
Chain: A
Fragment: Kinase Domain, Residues 604-898
Synonym: Developmentally-Regulated Eph-Related Tyrosine Kin Related Tyrosine Kinase, Eph Tyrosine Kinase 3, Eph-Like Ki Ek5, Hek5, Renal Carcinoma Antigen Ny-Ren-47, Tyrosine-Prot Tyro5, Tyrosine-Protein Kinase Receptor Eph-3, Ephb2, Ephhb
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 0.235 R_Free 0.263
length a length b length c angle alpha angle beta angle gamma
34.590 41.190 54.470 92.65 97.15 114.79
method X-Ray Diffractionresolution 2.27 Å
enzyme Transferase E.C. BRENDA

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] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (3zfm.pdb1.gz) 41 Kb
  • CSU: Contacts of Structural Units for 3ZFM
  • Structure Factors (214 Kb)
  • Retrieve 3ZFM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZFM from S2C, [Save to disk]
  • Re-refined 3zfm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZFM 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 3ZFM
  • 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 3ZFM, from MSDmotif at EBI
  • Fold representative 3zfm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zfm] [3zfm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ZFM: [TyrKc ] by SMART
  • Other resources with information on 3ZFM
  • Community annotation for 3ZFM at PDBWiki (http://pdbwiki.org)

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