Method 2: Search the Entrez Protein database for terms(s) of interest then follow the Related Structures link for the protein sequence record(s) of interest

• Use the Entrez Protein search page to retrieve protein sequence record(s) of interest.
  (The Entrez Help document provides search tips for the Entrez nucleotide and protein sequence databases.)
  For example, retrieve reference sequences for human prostaglandin synthase with a search such as:
  
  

  (prostaglandin[title] AND synthase[title]) AND human[organism] AND srcdb_refseq[properties]



• On the document summary (docsum) list of protein search results, open the Links menu for a record of interest and select the "Related Structure" option. That will retrieve similar protein sequences that are present in 3D structure records, as identified by the CBLAST program. The 3D structures might align to only a portion of the query sequence, and the Related Structures page will show the footprint(s) of the matching region(s).



• On the Related Structures page, click on the pink bar that represents the alignment footprint in the graphic display of hits to see an alignment between your query sequence and the structure-based protein sequences. (If you are viewing the table display of related structures rather than the graphic display, click on "[+]" beside the thumbnail image of any structure of interest to see an alignment of the structure's protein sequence to your query sequence.)



• On the sequence alignment display, press the View Structure and Alignment in Cn3D button to open an interactive view of the sequence alignment and corresponding 3D structure (illustrated example). The Cn3D program must be present on your computer in order for the button to work; the program is free and takes only a minutes to install.

Additional notes:

• If a sequence record in the Entrez Protein database was derived directly from a 3D structure record, the Links menu will contain a "Structure" option (which will take you directly to a summary page for the source structure record), in addition to the "Related Structure" option.



• If the Links menu for an individual protein sequence record does not contain an option for "Related Structure", then no structure-based protein sequences were similar enough to your protein of interest to pass the CBLAST score cutoff. However, other records in your protein search results might have a "Related Structure" link. Alternatively, you can BLAST the protein sequence against the PDB (structure) database and adjust the algorithm parameters to decrease the stringency of the search, if desired.

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See also: How to align a query protein to a similar sequence from a 3D structure and interactively view sequence/structure relationships.