1RD9 Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2 date
authors Pickens, J.C., Mitchell, D.D., Liu, J., Tan, X., Zhang, Z., Verlinde, C.L., Hol, W.G., Fan, E.
compound source
symmetry
R_factor
R_Free 0.18357
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.44
ligand BV2, P6G, TRS enzyme
related structures by homologous chain: 1MD2, 1RF2
Gene
Ontology
ChainFunctionProcessComponent
H, F, D, G, E
  • host cell surface binding
  • toxin activity


    • Primary referenceNonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer., Pickens JC, Mitchell DD, Liu J, Tan X, Zhang Z, Verlinde CL, Hol WG, Fan E, Chem Biol 2004 Sep;11(9):1205-15. PMID:15380181
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (197 Kb) [Save to disk]
  • Biological Unit Coordinates (1rd9.pdb1.gz) 191 Kb
  • LPC: Ligand-Protein Contacts for 1RD9
  • CSU: Contacts of Structural Units for 1RD9
  • Likely Quarternary Molecular Structure file(s) for 1RD9
  • Structure Factors (864 Kb)
  • Retrieve 1RD9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RD9 from S2C, [Save to disk]
  • Re-refined 1rd9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1RD9 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 1RD9
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1RD9 1RD9D 1RD9E 1RD9F 1RD9G 1RD9H from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RD9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rd9d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rd9e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1rd9f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1rd9g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1rd9h_, region H [Jmol] [rasmolscript] [script source]
  • 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: [1rd9_H] [1rd9_F] [1rd9] [1rd9_G] [1rd9_E] [1rd9_D]
  • SWISS-PROT database: [P01556]
  • Domain organization of [CHTB_VIBCH] by SWISSPFAM
    • Other resources with information on 1RD9
  • Community annotation for 1RD9 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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