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
Ec: 2.7.10.1
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
crystal
cell
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
ligand
enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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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