The generic numbering of PDZ-domains is based on the residue annotation used to describe the structure of the third PDZ domain of PSD-95 (Doyle, D. A., A. Lee, et al. (1996). "Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ." Cell 85(7): 1067-76.

PDZ domains typically consist of two a-helices, aA and aB, and six b-strands, bA to bF.

The residues in these secondary structure elements are named bA1, bA2 etc. Alignment of PDZ domain sequences with the third PDZ domain of PSD-95 extends this numbering scheme to all other known PDZ domains.

The residues of the peptide are commonly termed P-0, P-1, P-2 etc., where the terminal residue in the ligand interacting with the PDZ domain is termed the P-0 position, and the residue immediately N-terminal is named P-1, etc.

PDZBase can be queried using the generic numbering schemes described above.

To retrieve all PDZ-domains with a specific residue at a specific position:

enter the generic position and the specific residue type separated by a space,

e.g. “aB1 H” for all PDZ-domains with a histidine as the first residue in the second alpha-helix,

and “bB2 L” for all PDZ-domains with a leucine as the second residue of the second beta-strand.

[Note: Use a or b rather than a or b to indicate the generic position.]