Browse Pfams In PDB

The Browse button provides access to all PFAM domains identified in the PDB. Use the links to find families that begin with the chosen letter or number.

browse

The "Top 20" lists those 20 Pfam families that have the largest number of entries in the PDB. Clicking "Top 20" will produce this table:

Top 20

The column #Entry indicates how many PDB entries contain the Pfam, and the ModelLength is the length (number of match states) of the Pfam HMM model. You can select one Pfam ID, get a list of PDB entries which contains this Pfam. This is similar to "PFAM ID" search. For instance, click "Pkinase", and the table shown below appears; it lists all PDB entries with Pkinase domains (the image only shows a part of the list).

Pkinase

The columns PDBID, Pfam Arch (the Pfam chain architecture which contains the Pfam domain), E-Value and Entry Pfam Arch (the PFAM architecture of the entry) are sortable. SeqBeg and SeqEnd indicate the positions in the PDB sequence that mark the beginning and the end of the alignment with the Pfam HMM. Clicking one of the PDBIDs produces the table of Pfam architectures for that entry, similar to a PDBID search.