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.
1$\begingroup$ You know about PDB I guess? $\endgroup$– Chris_RandsJul 26, 2017 at 15:33
$\begingroup$ @Chris_Rands yeah PDB is great, but to me it seems a bit more like you need to know what you're looking for (ex. EGFR T790M with some kind of binding agent present). I'm looking more for almost a literal diagram or table of the gene detailing relevant functional and confirmation information in a more simplified way. Definitely a source I will be using though. $\endgroup$– DanJul 26, 2017 at 16:35
1$\begingroup$ Pfam might help too. $\endgroup$– JamesJul 27, 2017 at 2:57
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.
$\begingroup$ This seems like exactly what I was looking for, for some reason I haven't come across this in my searching. Seems very simple and to the point, also a plus that you can reference the db locally. Thanks! $\endgroup$– DanJul 26, 2017 at 16:38
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 188.8.131.520IPR012346
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.