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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.

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    $\begingroup$ You know about PDB I guess? $\endgroup$ – Chris_Rands Jul 26 '17 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. $\endgroup$ – Dan Jul 26 '17 at 16:35
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    $\begingroup$ Pfam might help too. $\endgroup$ – James Jul 27 '17 at 2:57
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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.

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  • $\begingroup$ 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! $\endgroup$ – Dan Jul 26 '17 at 16:38
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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  2.60.40.720IPR012346 
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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.
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