3 Dee - Database of Protein Domain Definitions

3Dee download area

Contents

• Lists of 3Dee domains
• Description of the file format
• References

• All domains stored in 3Dee
• Representatives from the domain families
• Representatives from the domain sequence families
• Representatives from the domain structure families

• All domains stored in the November 1999 release of 3Dee
[Download] (1041 kB).

List of all PDB files and the corresponding domain definitions that are included in the 3Dee database. Currently 3Dee is in line with the version of the PDB at the 21st July 1998. Note that domains which consist of segments from more than one chain, so called 'multi-chain domains', appear more than once in the list, as the 3Dee setup requires identical multi-chain domain definitions for each of these chains.

• Representatives from the domain families
[Download] (135 kB).

When sequence families are divided into similar domain organisation families, domains with significant sequence similarity may be separated. Therefore the representatives of the domain families do not make up a non-redundant set of sequences.

• Representatives from the domain sequence families
[Download] (85 kB).

Derived after clustering the representatives of the domain families by their sequence similarity; this is a non-redundant set of domain sequences.

• Representatives from the domain structure families
[0.1] (11 kB), [4.0] (47 kB), [5.0] (60 kB), [6.0] (72 kB).

The representatives from the domain sequence families are clustered at different thresholds of structural similarity calculated with the STAMP program. The representatives of the resulting domain structure families are a set of structurally non-redundant domains.

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 definition format consists of the following elements:

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

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.

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