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. 2011 Jan 24;6(1):e16047. doi: 10.1371/journal.pone.0016047

Figure 2. The PDZ binding pocket.

Figure 2

(A) PDZ binding pocket residues were identified through molecular modeling and sequence alignment (see file S4). We extracted the 16 residues and two flanking residues, previously identified to be of importance for ligand binding [14], [17]. (B) Consensus sequence of the amino acids in the binding pocket of class 1 PDZs as defined by Tonikian et al. [14] (n = 22). (C) Consensus sequence of human class 2 PDZs (n = 17). (D) Consensus sequence of the distribution of amino acids per position of all 15 species investigated in this study. No significant difference was found with the Homo sapiens consensus sequence. (E) Pair-wise clustering in 3D space of all 1704 PDZ binding pocket sequences identified illustrates specific clustering of metazoan PDZ sequences (red, yellow and green) and independent clustering of the majority of unicellular sequences (green). For a 2D image please see Fig. S3.