1MD2 Toxin date Aug 06, 2002
title Cholera Toxin B-Pentamer With Decavalent Ligand Bmsc-0013
authors Z.Zhang, E.A.Merritt, M.Ahn, C.Roach, W.G.J.Hol, E.Fan
compound source
Molecule: Cholera Toxin B Subunit
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
symmetry Space Group: C 1 2 1
R_factor 0.125
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.124 66.176 78.221 90.00 106.33 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand 233, S, SQ 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 referenceSolution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin., Zhang Z, Merritt EA, Ahn M, Roach C, Hou Z, Verlinde CL, Hol WG, Fan E, J Am Chem Soc 2002 Nov 6;124(44):12991-8. PMID:12405825
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (230 Kb) [Save to disk]
  • Biological Unit Coordinates (1md2.pdb1.gz) 203 Kb
  • CSU: Contacts of Structural Units for 1MD2
  • Likely Quarternary Molecular Structure file(s) for 1MD2
  • Structure Factors (1090 Kb)
  • Retrieve 1MD2 in mmCIF format [Save to disk]
    • View 1MD2 in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
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  • GRASS (Graphical Representation and Analysis of Structure Server)
  • Cartoon representation from PDB Cartoon
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    • Structure-derived information
  • Conformational Epitope Prediction for 1MD2 1MD2D 1MD2E 1MD2F 1MD2G 1MD2H from the CEP Server.
  • 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 1MD2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1md2d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1md2e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1md2f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1md2g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1md2h_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1md2 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: [1md2_E] [1md2_G] [1md2_F] [1md2_H] [1md2_D]
    • Other resources with information on 1MD2
  • InterPro: IPR001835
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
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