RNEDD4 WWIII domain from Rattus norvegicus
WW domains bind [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs. The PDB file with id 1i5h is a RNEDD4 WWIII domain bound to a ENaC peptide. For more information, please refer to the Kanelis et al (2011).
74 kDa type IV collagenase from Homo sapiens
The PDB file with id 1eak contains a complex of the catalytic domain of the type IV collagenase (gelatinase A MMP-2) complexed with an inhibitor peptide.
The binding site that PepSite predicts differs from the one shown in the complex, which resides in a central cavity of the protein, but is instead inside an exposed aromatic surface lying on one of the fibronectin domains of MMP2. This surface resembles that for many other proline-rich peptide binding proteins (e.g., SH3, EH1, etc.), and was originally suggested to be the binding site for gelatin based on an early single domain structure (Pickford et al., 1997) and alanine scanning mutagenesis in MMP9 (Bányai et al., 1994), which showed that residues near to our predicted site were important for gelatin binding. Subsequent studies have confirmed this gelatin binding site in MMP2 (e.g., Briknarová et al., 2001).
PIWI protein from Archaeoglobus fulgidus
Till et al. (2007) described a motif termed 'Argonaute hook' that binds argonaute (Ago) proteins through their PIWI domains. Ago proteins mediate silencing of nucleic acids by small RNAs. The authors showed that a PIWI domain pocket that binds the 5' end of interfering RNAs is required for Ago hook binding.
If you compare the predictions with the PDB structure 1ytu you can see the predicted peptide binding site overlaps with the RNA, as mentioned in Till et al. (2007). The peptide motif shown to bind was D/N-E/N-π-S/T-π-A/G-W-G-E (where π denotes polar residues), and actually two copies of this. As in the PepSite web server only peptides of length up to 10 residues are currently allowed, we used in this example only one copy, i.e., PDNGTSAWGE.