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Structures
module of the MLA course on Introduction to Molecular Biology Information
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Using Front Door #2:
Link from P53 Tumor Suppressor Protein Sequence Records to Structure Record

 
Another way to easily access 3-D structures is to start a search in the Entrez Protein database for a topic of interest, then jump to the Entrez Structure database to retrieve associated records.
 

 
Front Door #2 Search the Entrez Protein database and then "Display" the associated Structure records.
Note: Any protein sequence that was extracted from a 3-D structure record will have a "Structure" option in its "Links" menu. Rather than opening the Links menu of each protein sequence in your search results, a quick way to find all the associated structure records is to use the "Structure Links" option in the "Display" menu near the top of the search results page.
Example:  Search Entrez Protein for:

P53 Tumor Suppressor

Select "Structure Links" from the "Display" menu near the top of the search results page.
 
 

 
  • search the Entrez Protein database for:   P53 Tumor Suppressor  

  • the document summary ("docsum") page gives brief title listings for the records your retrieved. The last line of each listing is the "FASTA-formatted sequence identifier". It includes:
    • the GI number of the protein sequence
    • the source database, indicating to which subset of Entrez Proteins the record belongs(e.g., "gb" for GenBank translation; "ref" for refseq"; "pdb" for "Protein Data Bank"; etc.)
    • the accession number of the record from which the sequence was extracted
    • if the protein sequence is from a structure record that contains multiple protein chains (e.g., A, B, C), the protein chain will be indicated after the accession number. (E.g., The 1TUP structure is made from 3 protein chains: A, B, and C. The sequence of each chain was extracted into its own protein record. All three protein records point back to the same 3-D structure: 1TUP.)

  • the presence of the letters "pdb" in the FASTA-formatted sequence identifier are the clue to knowing that these sequence records have an associated, resolved structure

  • follow the "Structure" option in the "Links" menu for any one of the three structures to view the corresponding structure record.

(Note: The Links menu also contains an option for "3D Domains". Those are derived from components of structure records. More information about 3D Domains is provided in the Resource Guide)

 


Structures
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Revised 11/06/2007