A structural domain is a level of organization that is intermediate between secondary structure and tertiary structure. For single domain structures, a structural domain can be thought of as being equivalent to the tertiary structure, with the caveat that long, disordered regions might be excluded. The sense of 'order' and 'organization' is central to the concept of a structural domain. Unfortunately, there is no single, accepted definition of a structural domain in proteins, so we rely on several definitions in order to provide a practical solution to the problem. In PDBj Mine we provide links to both the SCOP and CATH databases which give domain definitions for a large number of PDB entries using rather well accepted methods. In Structure Navigator we also utilize the program Protein Domain Parser ( PDP ) for entries that lack SCOP or CATH definitions.