I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms of either specific residue ranges, genomic coordinates, etc. Ideally, the database would include 3D conformational information as well as the functional domains. Does such a database exist? It seems that this information can be inferred for a given protein using various publications and references but I have yet to find a single collection containing these data all in one place.
Some of this information (at least some domains, active sites, etc) is available from UniProt.
If you want to download their whole database, you can search without specifying any terms and then click the Download button.
EnsEMBL also has this. Search for your gene of interest, choose your transcript, go to the page of its protein product(s), and select "Domains & Features" from the right-hand menu (using human p53 as an example):
Domain source Start End Description Accession InterPro PANTHER 3 331 - PTHR11447:SF6- Pfam 5 29 p53 transactivation domain PF08563 IPR013872 PANTHER 3 331 p53 tumour suppressor family PTHR11447 IPR002117 PRINTS 116 142 p53 tumour suppressor family PR00386 IPR002117 PRINTS 158 179 p53 tumour suppressor family PR00386 IPR002117 PRINTS 213 234 p53 tumour suppressor family PR00386 IPR002117 PRINTS 236 258 p53 tumour suppressor family PR00386 IPR002117 Prosite_patterns 237 249 p53 tumour suppressor family PS00348 IPR002117 PRINTS 264 286 p53 tumour suppressor family PR00386 IPR002117 Pfam 95 288 p53 DNA-binding domain PF00870 IPR011615 Superfamily 97 287 p53-like transcription factor DNA-binding SSF49417 IPR008967 Gene3D 94 297 p53/RUNT-type transcription factor DNA-binding domain 18.104.22.1680IPR012346
In addition to UniProt and EnsEMBL as suggested above you might like:
- InterPro, functional analysis of proteins by classifying them into families and predicting domains and important sites.
- ECOD, a classification of protein domains by evolutionary relationship.
- Pfam, a collection of protein families.
- CATH, protein structural domains.
- Genome3D, which combines various resources to structurally annotate proteins.