Antibodies are glycoproteins belonging to the immunoglobulin superfamily.
Three-dimensional structures have been established from x-ray crystallography
as listed in http://www.bioinf.org.uk/abs/sacs/.
Anti-carbohydrate antibodies with specificity to oligosaccharides and
polysaccharides are of a high importance in immunology and vaccine development (1).
The present data base is concerned with the limited set of
high resolution structures of carbohydrate-antibody complexes.
Analysis of these complexes reveals general trends about how antibodies
recognize different types of carbohydrates. Antibodies which recognize
a terminal carbohydrate motif generally feature cavity-like binding sites,
where one or more carbohydrate residues are anchored in the cavity by “end-on” extension.
Antibodies which recognize an internal carbohydrate motif,
as a single repeat of a bacterial polysaccharide for example)
generally exhibit groove-like binding sites, or very large cavities
which are open at both ends of the site, allowing for “side-on” entry of the antigen.
Data Query
Upon reaching the search page, two buttons to query the data base appear*
on the left hand panel: Simple search and Advanced Search.
Simple Search
A right click opens a window on “Antibody information”.
Advanced Search
Under the name “Select Criteria” a search box offers to select among the following items:
nomenclature
antibodyoriginimmunoglobulin type
A search box is provided in which appears a drop-down button
enlisting all the entries corresponding to the selected item.
The result is prompt to guide the user in selecting the “hits”
found in the data base, by a simple search engine.
More complex search can be made by combining criteria which
can be combined from up to four search boxes. A preview of the results
is displayed. The amount of information provided allows the user to make
an informed choice prior going to “Antibody Information”.
Results
The detailed results are available under two tabs: “Antibody Information” and “Display and Download”.
Antibody Information
Under the button: “Antibody Information” are given: origin, name of the antibody,
nomenclature of the bound carbohydrate, PDB code, resolution, comment,
immunoglobulin class, reference to the original article. Provision is also given
to view a still three-dimensional ribbon type representation of
the three-dimensional structure.
Links to Medline (www.ncbi.nlm.nih.gov/pubmed)
and Protein Data Base (www.rcsb.org) are also provided.
Display and Download
On this page, is given a three-dimensional representation of the three-dimensional
structure of the complex which has been constructed from the reported atomic
coordinates with the help of the PyMol molecular visualisation system.
In the case of MAbs – carbohydrate crystalline complexes, a particular emphasis
is given to indicate the conformation of the bound carbohydrate which can be viewed.
The two three-dimensional structures 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.