1RDP Toxin date Nov 05, 2003
title Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand Bv3
authors J.C.Pickens, D.D.Mitchell, J.Liu, X.Tan, Z.Zhang, C.L.Verlinde, W.G.Hol, E.Fan
compound source
Molecule: Cholera Toxin B Protein (Ctb)
Chain: D, E, F, G, H
Engineered: Yes
 Organism_scientific: Vibrio Cholerae
Organism_common: Bacteria
Gene: Ctxb
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_strain: Top10
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad
symmetry Space Group: C 1 2 1
R_factor 0.130
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.090 66.079 78.715 90.00 105.83 90.00
method X-Ray Diffractionresolution 1.35 Å
ligand BV3, PGE, TMN enzyme
similarity Belongs to the Enterotoxin_b family.
subunit The a subunit contains two chains, a1 and a2, linked by a disulfide bridge. The holotoxin (choleragen) consists of a pentameric ring of b subunits whose central pore is occupied by the a subunit.
gene ctxB (V. cholerae)
function It can bind five gm1 gangliosides. The b subunit pentameric ring directs the a subunit to its target by binding to the gm1 gangliosides present on the surface of the intestinal epithelial cells. It has no toxic activity by itself.
Gene
Ontology
ChainFunctionProcessComponent
H, F, D, G, E
  • pathogenesis
  • extracellular region
  • membrane
    • 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] (217 Kb) [Save to disk]
  • Biological Unit Coordinates (1rdp.pdb1.gz) 191 Kb
  • CSU: Contacts of Structural Units for 1RDP
  • Likely Quarternary Molecular Structure file(s) for 1RDP
  • Structure Factors (1031 Kb)
  • Retrieve 1RDP in mmCIF format [Save to disk]
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    • Structure-derived information
  • Conformational Epitope Prediction for 1RDP 1RDPD 1RDPE 1RDPF 1RDPG 1RDPH from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
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  • 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]
  • Fold representative 1rdp 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: [1rdp_H] [1rdp_G] [1rdp_F] [1rdp_D] [1rdp_E]
    • Other resources with information on 1RDP
  • InterPro: IPR001835
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