1MD2 CHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013 date
authors Zhang, Z., Merritt, E.A., Ahn, M., Roach, C., Hol, W.G.J., Fan, E.
compound source
symmetry
R_factor
R_Free 0.16432
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.45
ligand 233, CSS, CYN, SQ enzyme
related structures by homologous chain: 1PZJ, 1RD9
Gene
Ontology
ChainFunctionProcessComponent
H, F, D, G, E
  • host cell surface binding
  • toxin activity


  • 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] (208 Kb) [Save to disk]
  • Biological Unit Coordinates (1md2.pdb1.gz) 202 Kb
  • LPC: Ligand-Protein Contacts for 1MD2
  • CSU: Contacts of Structural Units for 1MD2
  • Likely Quarternary Molecular Structure file(s) for 1MD2
  • Structure Factors (1139 Kb)
  • Retrieve 1MD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MD2 from S2C, [Save to disk]
  • Re-refined 1md2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1MD2 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 1MD2
  • Ramachandran plot from PDBSum
  • 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
  • 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]
  • 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_F] [1md2_H] [1md2_G] [1md2] [1md2_E] [1md2_D]
  • SWISS-PROT database: [P01556]
  • Domain organization of [CHTB_VIBCH] by SWISSPFAM
  • Other resources with information on 1MD2
  • Community annotation for 1MD2 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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