2BBA Signaling Protein date Oct 17, 2005
title Crystal Structure And Thermodynamic Characterization Of The Receptor In Complex With An Ephrin-B2 Antagonist Peptide Re Determinants For Receptor Specificity.
authors J.E.Chrencik, P.Kuhn, Accelerated Technologies Center For Gene Structure (Atcg3d)
compound source
Molecule: Ephrin Type-B Receptor 4
Chain: A
Fragment: Ligand Binding Domain
Synonym: Tyrosine-Protein Kinase Receptor Htk
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ephb4, Htk
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Hii-5
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbac6

Molecule: Agonist Peptide
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: P 41 21 2
R_factor 0.174 R_Free 0.191
length a length b length c angle alpha angle beta angle gamma
60.972 60.972 151.681 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand SO4 enzyme Transferase E.C. BRENDA
note 2BBA is a representative structure
Primary referenceStructure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity., Chrencik JE, Brooun A, Recht MI, Kraus ML, Koolpe M, Kolatkar AR, Bruce RH, Martiny-Baron G, Widmer H, Pasquale EB, Kuhn P, Structure. 2006 Feb;14(2):321-30. PMID:16472751
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (2bba.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 2BBA
  • CSU: Contacts of Structural Units for 2BBA
  • Likely Quarternary Molecular Structure file(s) for 2BBA
  • Structure Factors (217 Kb)
  • Retrieve 2BBA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BBA from S2C, [Save to disk]
  • Re-refined 2bba structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BBA 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 2BBA
  • 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 2BBA, from MSDmotif at EBI
  • Fold representative 2bba from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bba] [2bba_P] [2bba_A]
  • SWISS-PROT database: [P54760]
  • Domain organization of [EPHB4_HUMAN] by SWISSPFAM
  • Domain found in 2BBA: [EPH_lbd ] by SMART
  • Other resources with information on 2BBA
  • Community annotation for 2BBA at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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