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Luhua,

HIV protease is a good example. The binding site are made of a pair
of catalytic triad of Gly, Asp, and Thr. and two beta sheet loops.
When it is free of ligand binding, the two loops are open. They are
moved about 4 Angstroms Upon binding to a inhibitor, to cover up
the binding cavity. You can find the crystal structures of both
in free and bounded form. I do not quite remember the file names.
let me know if you have difficulty finding it at pdb site.

Another one would be antibody binding to antigen. I know much less
in this case. Just a suggestion.

Best regards!
-- 
Willie Cui			voice: 201-512-0486
MicroSimulations		fax:   201-512-0489
478 Green Mountain Road		email: [email-masked]
Mahwah, NJ 07430		URL:   http://www.microsimulations.com
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