2QBX Signaling Protein date Jun 18, 2007
title Ephb2snew Antagonistic Peptide Complex
authors J.E.Chrencik, A.Brooun, M.I.Recht, G.Nicola, E.B.Pasquale, P.Kuhn, Accelerated Technologies Center For Gene To 3d Structure (Atcg3d)
compound source
Molecule: Ephrin Type-B Receptor 2
Chain: A, B
Fragment: Ephb2
Synonym: Tyrosine-Protein Kinase Receptor Eph-3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ephb2, Drt, Epht3, Epth3, Erk, Hek5, Tyro5
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Hi-5
Expression_system_vector_type: Pfastbac1
Expression_system_plasmid: Pbac6

Molecule: Antagonistic Peptide
Chain: D, P
Engineered: Yes

Synthetic: Yes
Other_details: Antagonistic Peptide
symmetry Space Group: P 32
R_factor 0.194 R_Free 0.270
length a length b length c angle alpha angle beta angle gamma
40.183 40.183 235.025 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand SO4 enzyme Transferase E.C. BRENDA
Primary referenceThree-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition., Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, Pasquale EB, Kuhn P, J Biol Chem. 2007 Dec 14;282(50):36505-13. Epub 2007 Sep 26. PMID:17897949
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (2qbx.pdb1.gz) 34 Kb
  • Biological Unit Coordinates (2qbx.pdb2.gz) 34 Kb
  • Biological Unit Coordinates (2qbx.pdb3.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 2QBX
  • CSU: Contacts of Structural Units for 2QBX
  • Likely Quarternary Molecular Structure file(s) for 2QBX
  • Structure Factors (273 Kb)
  • Retrieve 2QBX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QBX from S2C, [Save to disk]
  • Re-refined 2qbx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QBX 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 2QBX
  • 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 2QBX, from MSDmotif at EBI
  • Fold representative 2qbx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qbx] [2qbx_B] [2qbx_D] [2qbx_A] [2qbx_P]
  • SWISS-PROT database: [P29323]
  • Domain organization of [EPHB2_HUMAN] by SWISSPFAM
  • Domain found in 2QBX: [EPH_lbd ] by SMART
  • Other resources with information on 2QBX
  • Community annotation for 2QBX 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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