1B4F Signal Transduction date Dec 20, 1998
title Oligomeric Structure Of The Human Ephb2 Receptor Sam Domain
authors C.D.Thanos, K.E.Goodwill, J.U.Bowie
compound source
Molecule: Ephb2
Chain: A, B, C, D, E, F, G, H
Fragment: Sam Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Vascular
Cell: Renal Microvascular Endothelial
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: P 41
R_factor 0.228 R_Free 0.273
length a length b length c angle alpha angle beta angle gamma
73.897 73.897 104.547 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
related structures by homologous chain: 1F0M
Primary referenceOligomeric structure of the human EphB2 receptor SAM domain., Thanos CD, Goodwill KE, Bowie JU, Science 1999 Feb 5;283(5403):833-6. PMID:9933164
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (1b4f.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (1b4f.pdb2.gz) 57 Kb
  • CSU: Contacts of Structural Units for 1B4F
  • Likely Quarternary Molecular Structure file(s) for 1B4F
  • Structure Factors (961 Kb)
  • Retrieve 1B4F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1B4F from S2C, [Save to disk]
  • Re-refined 1b4f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1B4F 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 1B4F
  • 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 1B4F, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1b4fa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1b4fb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1b4fc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1b4fd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1b4fe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1b4ff_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1b4fg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1b4fh_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1b4f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1b4f_D] [1b4f] [1b4f_H] [1b4f_B] [1b4f_G] [1b4f_C] [1b4f_E] [1b4f_F] [1b4f_A]
  • SWISS-PROT database: [P29323]
  • Domain organization of [EPHB2_HUMAN] by SWISSPFAM
  • Domain found in 1B4F: [SAM ] by SMART
  • Other resources with information on 1B4F
  • Community annotation for 1B4F 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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