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The Antibody-Antigen Complex

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Structural Features

The Antibody-Antigen Interaction
The molecule above is a complex between a single Fab unit and the small molecule phenyl [1-(1-N-succinylamino)pentyl]-2-phosphonate (J. Guo, W. Huang, and T. S. Scanlan, J. Amer. Chem. Soc., 116, 6062, (1994)).

the structure of the antigen bound to the antibody

Note that the antigen rests in a very tight binding pocket which is exactly the right size and shape to receive it.  This is one reason for the underlying specificity of the antibody-antigen interaction - the lock and key hypothesis.  Other important factors include enthalpic contributions from van der Waals interactions and hydrogen bonds, and entropic contributions from the release of bound water upon antigen binding.  The model presented above is only a small part of the antibody molecule containing the antigen binding site, one L chain and a fragment of one H chain.  This Fab fragment contains several disulphide bonds, although only one of them is involved in holding the H and L chains together.