3did: interacting protein domains of known three-dimensional structure

Abstract

The database of 3D Interacting Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur. It also offers an overview of how similar in structure are interactions between different members of the same protein family. The database also contains Gene Ontology-based functional annotations and interactions between yeast proteins from large-scale interaction discovery studies. A web-based tool to query 3did is available at http://3did.embl.de.

Figure 1

Network of interacting domains. The domain of interest (e.g. Alpha-amylase) is shown as a rhombus and the interacting domains as ellipses. By default, the interaction graph is colored randomly, but it can be colored based on functional GO terms. Bold lines represent intra-chain interactions (i.e. between domains in the same protein), thin lines indicate inter-chain interactions (i.e. between domains in different proteins) and dashed lines show interactions where both types have been seen. The network depth can be changed to include indirect interactions.

Figure 2

Example of the information given for two interacting domains. The table shows a subset of the structures where this interaction is present, with information on the location of the interacting domains (PDB numbering) as well as the interaction scores as described previously (13). By clicking at the rasmol icon, the user will get a 3D display of the complex with the two interacting domains shown in ribbons and the contacting residues in ball-and-stick (magnification top). Where possible, there are also links to SimInt showing how conserved is the interaction type (magnification bottom) and to yeast proteins found experimentally to interact that contain these domains.

Figure 3

Graph of the COX complex. This shows the protein chains contained in the structure (PDB code 2occ) and the interacting domains referenced in 3did. For multiple copies of the complex, chains containing the same domains are grouped into one block. Lines connecting the domains show both inter- and intra-chain interactions as in Figure 1.