3 Dee - Database of Protein Domain Definitions

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This page contains links to lists of domains from different levels within the 3Dee sequence and structural hierarchy and a description of their format. Please cite the references describing 3Dee in the literature if you use the data provided on this page for your work. A technical report of the 3Dee database outlining its levels of data representation is available online.


Lists of 3Dee domains

Description of the file format

Domain entries in 3Dee are stored in STAMP format. In each file, the first column contains the name of the PDB file, the second column the domain identifier and the expression in curly brackets the actual domain definition, e.g.
pdb1gdh.ent 1gdha-1-AS     { A 2 _ to A 100 _ A 290 _ to A 321 _ }
            1gdha-2-AS     { A 101 _ to A 289 _ }
            1gdhb-1-AS     { B 2 _ to B 100 _ B 290 _ to B 321 _ }
            1gdhb-2-AS     { B 101 _ to B 289 _ }

The domain identifier consists of a four letter PDB code, a chain identifier, the initials of the database annotator who has defined the domain and a revision number, if more than one revision exists. For example 2mysa-4-AS.2 refers to the fourth domain of the 'a' chain of protein 2mys; it is the second revision of the domain definition produced by AS. The annotator's initials may be replaced by the terms DOMAK or AUTO that represent automatic domain definition methods. DOMAK locates domains for a given set of co-ordinates, while AUTO is using sequence similarity to chains with known domain boundaries.

The domain definition format consists of the following elements:

[chain id.] [res. number1] [ins. code1] to [chain id.] [res. number2] [ins. code2].


If you use one of the datasets above, please cite the descriptions of the 3Dee database in the literature:
  1. Dengler, U., Siddiqui, A. S. & Barton, G. J. (2001). Protein structural domains: Analysis of the 3Dee domains database. Proteins 42, 332-344.

  2. Siddiqui, A. S., Dengler, U. & Barton, G. J. (2001). 3Dee: A database of protein structural domains. Bioinformatics 17, 200-201.

Last revised 01 November 2000
Comments to Uwe Dengler
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, UK