Using Front Door #2: Link from P53 Tumor Suppressor Protein Sequence
Records to Structure Record
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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.
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| 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.
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Example: Search Entrez Protein for:
P53 Tumor Suppressor
Select "Structure Links" from the "Display" menu near the top of the search results page. |
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- 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)
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