3ZFX Transferase date Dec 12, 2012
title Crystal Structure Of Ephb1
authors J.E.Debreczeni, R.Overman, C.Truman, M.Mcalister, T.K.Attwood
compound source
Molecule: Ephrin Type-B Receptor 1
Chain: A, B, C, D, E, F, G, H, I
Fragment: Kinase Domain
Synonym:, Elk, Eph Tyrosine Kinase 2, Eph-Like Kin Ek6, Hek6, Neuronally-Expressed Eph-Related Tyrosine Kinas Tyrosine-Protein Kinase Receptor Eph-2, Ephb1;
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: Plasmid
symmetry Space Group: P 32
R_factor 0.18835 R_Free 0.21669
length a length b length c angle alpha angle beta angle gamma
195.980 195.980 60.242 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand SO4 enzyme Transferase E.C. BRENDA
F, A, E, B, H, C, D, I, G

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] (745 Kb) [Save to disk]
  • Biological Unit Coordinates (3zfx.pdb1.gz) 91 Kb
  • Biological Unit Coordinates (3zfx.pdb2.gz) 84 Kb
  • Biological Unit Coordinates (3zfx.pdb3.gz) 82 Kb
  • Biological Unit Coordinates (3zfx.pdb4.gz) 89 Kb
  • Biological Unit Coordinates (3zfx.pdb5.gz) 87 Kb
  • Biological Unit Coordinates (3zfx.pdb6.gz) 84 Kb
  • Biological Unit Coordinates (3zfx.pdb7.gz) 85 Kb
  • Biological Unit Coordinates (3zfx.pdb8.gz) 89 Kb
  • Biological Unit Coordinates (3zfx.pdb9.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 3ZFX
  • CSU: Contacts of Structural Units for 3ZFX
  • Structure Factors (1388 Kb)
  • Retrieve 3ZFX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZFX from S2C, [Save to disk]
  • Re-refined 3zfx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZFX 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 3ZFX
  • 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 3ZFX, from MSDmotif at EBI
  • Fold representative 3zfx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zfx_D] [3zfx_F] [3zfx_E] [3zfx_H] [3zfx_A] [3zfx] [3zfx_C] [3zfx_B] [3zfx_G] [3zfx_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ZFX: [TyrKc ] by SMART
  • Other resources with information on 3ZFX
  • Community annotation for 3ZFX at PDBWiki (http://pdbwiki.org)

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