How good is a Homology Model? Side-Chain Flexibility

Side chains orientations: most were reasonably well predicted.

For the trytophane residue at the tip of CDR3, different conformations were predicted: The side chain could pack into the relatively hydrophobic antigen binding pocket, blocking access to a solvent filled cavity underneath, or open up to allow an antigen to bind into the pocket. Indeed the two crystal structures showed a differed in the conformation of this residue: in the isopropanol structure, the tryptophane side chain is inside the binding pocket, while in the methane-pentane-diol structure the tryptophane is in an "open" conformation and a molecule of mpd sits in the bottom of the binding pocket.