Fig. 1. Structure of the PDZ domain and mechanism of peptide recognition. (A) Ribbon diagram of PSD-95 PDZ domain 3 (residues 306-394, shown in red) with a bound peptide (NH2-KQTSV-COOH, shown in blue). Names of ß-strands and 
-helices are indicated. The side chains of the peptide P0 residue (valine) and P-2 residue (threonine) are shown in stick form, as is the terminal carboxylate. (B) Diagram of the peptide-binding pocket. Residues in the PDZ-domain-binding pocket are shown in black; the peptide is shown in blue. Hydrogen bonds are drawn as red dotted lines, and hydrophobic packing is indicated by green arcs. (C) Solvent-accessible surface representation of the structure shown in (A) (probe radius=1.4 Å). The peptide is drawn as in A, and key binding pockets are indicated by circles (Doyle et al., 1996).
