4BKF Transferase date Apr 24, 2013
title Crystal Structure Of The Human Epha4 Ectodomain In Complex W Ephrinb3
authors E.Seiradake, A.Schaupp, D.Del Toro Ruiz, R.Kaufmann, N.Mitakidis K.Harlos, A.R.Aricescu, R.Klein, E.Y.Jones
compound source
Molecule: Ephrin Type-A Receptor 4
Chain: A, B
Fragment: Hepha4 Ectodomain, Residues 20-547
Synonym: Eph-Like Kinase 8, Ek8, Hek8, Tyrosine-Protein Kin Tyrosine-Protein Kinase Receptor Sek;
Ec: 2.7.10.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phlsec

Molecule: Ephrin-B3
Chain: C, D
Fragment: Hephrina5 Receptor Binding Domain, Residues 27-16
Synonym: Eph-Related Receptor Transmembrane Ligand Elk-L3, Related Receptor Tyrosine Kinase Ligand 8, Lerk-8;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phlsec
symmetry Space Group: P 43 3 2
R_factor 0.327 R_Free 0.351
crystal
cell
length a length b length c angle alpha angle beta angle gamma
300.530 300.530 300.530 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.65 Å
ligand
enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceStructurally encoded intraclass differences in EphA clusters drive distinct cell responses., Seiradake E, Schaupp A, Del Toro Ruiz D, Kaufmann R, Mitakidis N, Harlos K, Aricescu AR, Klein R, Jones EY, Nat Struct Mol Biol. 2013 Jun 30. doi: 10.1038/nsmb.2617. PMID:23812375
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (441 Kb) [Save to disk]
  • Biological Unit Coordinates (4bkf.pdb1.gz) 432 Kb
  • CSU: Contacts of Structural Units for 4BKF
  • Structure Factors (419 Kb)
  • Retrieve 4BKF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BKF from S2C, [Save to disk]
  • Re-refined 4bkf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BKF 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 4BKF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4BKF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bkf_D] [4bkf_B] [4bkf_C] [4bkf_A] [4bkf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4BKF: [EPH_lbd] [Ephrin_rec_like] [FN3 ] by SMART
  • Other resources with information on 4BKF
  • Community annotation for 4BKF at PDBWiki (http://pdbwiki.org)

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