• Data Base Content

    Lectins are oligomeric proteins that can specifically recognize carbohydrates, which as per present knowledge act as macromolecular tools to decipher sugar-encoded message. Among the proteins that interact non-covalently with carbohydrates, lectins bind mono- and oligosaccharides reversibly and specifically while displaying no catalytic or immunological activity.

    More than 1000 lectin three-dimensional structures are available in the database. Most of them have been determined by x-ray diffraction, although some neutron diffraction structures are available as well as NMR solution structures or theoretical models.
    About 70% of these structures have been determined in complex with a carbohydrate ligand; ranging from monosaccharides, to oligosaccharides or glycoproteins. This consists therefore in a very large amount of information about the molecular basis of carbohydrate recognition by lectins.

  • Data Query

    Upon reaching the search page form Glyco3D or directly from http://lectin3d.cermav.cnrs.fr/search.php, two buttons to query the data base appear on the left hand panel : Simple search and Advanced Search.
  • Simple Search

    The classification of the lectins is made based on their origin:
    1. algea;
    2. animal;
    3. bacteria;
    4. fungi and yeast;
    5. plant;
    6. virus.
    Upon selecting one family, a right click opens a new menu that prompts the user to choose among a sub-classification based on the fold family, then on the species of organisms. A further right click opens a new menu that contains all the three-dimensional structures of the selected lectin either in the apo state or complexed with ligand. A preview of the results is displayed in an accordion fashion, whereby the PDB code, the species, the resolution at which the structure has been solved, and the reference to the original publication are given.
    The amount of information provided allows the user to make an informed choice prior going to “Lectin Information”.
  • Advanced Search

    Under the name “Select Criteria”, a search box offers to select among the following items:
    1. species
    2. family
    3. sugars
    4. PDB
    5. ligands
    6. authors
    7. sequence
    A search box is provided in which appears a drop-down button enlisting all the entries corresponding to the selected item. For other items, the menu guides the user in selecting the “hits” found in the data base, by a simple search engine. More complex search can be made by combining up criteria from up to four search boxes.
  • Results

    The detailed results are available under two tabs: “Lectin Information” and “Display and Download”.
  • Lectin Information

    Under the button: “Lectin Information” is given: Origin, Class, Family, Species, PDB code, Resolution, Comment, and Reference. The comment section indicates whether the lectin has been solved in the form of a protein-carbohydrate complex. In that case, the nature of sugar is indicated along with its sequence. Provision is also given to view an image of the source of the protein, along with a still three-dimensional ribbon type representation of the three-dimensional structure, together with access to original 3D information at the Protein Data base. Links to NIH sites for references and taxonomy are also provided
  • Display and Download

    On this page, is represented one or more graphical representation of the lectin, or of the binding site with carbohydrate ligands, that have been constructed from the reported atomic coordinates with the help of PyMol software (www.pymol.org). A particular emphasis is given to indicate the location and conformation of the bound carbohydrate. The three-dimensional structure can be displayed under Jmol applet windows that enable basic viewing and measurements options. The atomic coordinates at the PDB can be downloaded for further use.

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