I am looking for databases that has compiled all the 3D structures of anitgen-antobody interations and provides details of the chemical interactions between them.
Also, please refer to papers that may use computation to study these interactions.
I don't know of a public database like what you are looking for, however if you search the literature and find some universities that are working on this field and have the device needed to evaluate Ag-Ab binding, many times they have private databases that you can access if you do work with the researcher. That is how I would approach this question. Also, some of the big antibody mfg in the world will get binding data on their popular antibodies, so you sometimes will see the binding values in catalogs online (i.e. Sigma, Novus, etc). Hope that helps.
All antibody-antigen complex 3D structures in the public domain are collected in the pdb https://www.rcsb.org/pdb or https://www.ebi.ac.uk/pdbe (as are all other macromolecular structures). You can search these in a variety of ways to extract and analyze the structures of interest.
You may want to consult the list of antibody resources published by the antibody society:
https://www.antibodysociety.org/web-resources/
SAbDab is a subset of the PDB containing only antibody structures (http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/)
abYbank / AbDb http://www.abybank.org/abdb/
Summary of Antibody Structures in the Protein Databank
http://www.bioinf.org.uk/abs/sacs/
For more, follow links or search the web.
The Immune Epitope Database (IEDB) at https://www.iedb.org/ has "Browse by 3D Structure" under its "Specialized Searches" options menu.
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