The function of antibodies involves specific binding to antigens, which induces an immune response by activation of various components of the adaptive immune system. The adaptive system uses two routes in immune defense: The antibody-mediated system and T cell mediated system. The binding of an antibody to the antigen takes place through a number of non-covalent specific interactions involving amino acid residues within the binding sites on the antigen (the epitope), and the antibody (the paratope). For the understanding of the mechanism of recognition of an antigen by an antibody and the role of different amino acid residues as the structural determinants of specificity of the interactions, a high resolution structure of the antibody-antigen complex is essential.
Four polypeptide chains, two so-called heavy (H) and two identical light (L) chains build up the antibody molecule. The heavy chain contains four domains while the light chain contains only two. The two N-terminal domains of the heavy and light chains associate with each other and build up the so-called Fab fragment, which can be obtained experimentally after a proteolitic cleavage of the heavy chain. On top of the Fab is the variable region which consists of four complementarity-determining regions (CDR), all within the N-terminal domains of the light and heavy chains. The CDRs function as the antigenic determinant responsible for antigen binding. They are also the least conserved (most variable) parts of the sequences of the light and heavy chains. For this reason the domains of the antibody containing the CDRs are called the variable domains (VH and VL). In contrast, the part of the heavy chain, which contains the two C-terminal domains, is called the constant region, or constant domain (C).