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 Ec: 2.7.1.112 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
crystal cell	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 Diffraction	resolution	1.65 Å
ligand	SO4	enzyme	Transferase E.C.2.7.1.112 BRENDA
note	2BBA is a representative structure
Primary reference	Structure 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 (229 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2bba_P] SWISS-PROT database: [P54760] Domain organization of [EPHB4_HUMAN] by SWISSPFAM Domain found in 2BBA: [EPH_lbd ] by SMART Alignments of the sequence of 2BBA with the sequences similar proteins can be viewed for 2BBA's classification [EPHB4_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [EPHB4_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2BBA

Community annotation for 2BBA at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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