1RDP Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3 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 0.17052
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.35
ligand BV3, PGE, TRS enzyme
related structures by homologous chain: 1DJR, 1PZK
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] (191 Kb) [Save to disk]
  • Biological Unit Coordinates (1rdp.pdb1.gz) 185 Kb
  • LPC: Ligand-Protein Contacts for 1RDP
  • CSU: Contacts of Structural Units for 1RDP
  • Likely Quarternary Molecular Structure file(s) for 1RDP
  • Structure Factors (1059 Kb)
  • Retrieve 1RDP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RDP from S2C, [Save to disk]
  • Re-refined 1rdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RDP 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 1RDP
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1RDP 1RDPD 1RDPE 1RDPF 1RDPG 1RDPH from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RDP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rdpd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rdpe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1rdpf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1rdpg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1rdph_, 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: [1rdp_F] [1rdp_D] [1rdp_H] [1rdp_G] [1rdp] [1rdp_E]
  • SWISS-PROT database: [P01556]
  • Domain organization of [CHTB_VIBCH] by SWISSPFAM
  • Other resources with information on 1RDP
  • Community annotation for 1RDP 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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