Figure 2. The Structure Summary page.

Figure 2The Structure Summary page

The page consists of three parts: the header, the view bar, and the graphic display. The header contains basic identifying information about the record: a description of the protein (Description:), the author list (Deposition:), the species of origin (Taxonomy:), literature references (Reference:), the MMDB-ID (MMDB:), and the PDB code (PDB:). Several of these data serve as links to additional information. For example, the species name links to the Taxonomy browser, the literature references link to PubMed, and the PDB code links to the PDB Web site. The view bar allows the user to view the structure record either as a graphic with Cn3D or as a text record in either ASN.1, PDB (RasMol), or Mage formats. The latter can also be downloaded directly from this page. The graphic display contains a variety of information and links to related databases: (a) The Chain bar. Each chain of the molecule is displayed as a dark bar labeled with residue numbers. To the left of this bar is a Protein hyperlink that takes the user to a view of the protein record in Entrez Protein. The bar itself is also a hyperlink and displays the VAST neighbors of the chain. If a structure contains nucleotide sequences, they are displayed in the order contained in the PDB record. A Nucleotide hyperlink to their left takes the user to the appropriate record in Entrez Nucleotide. (b) The VAST (3D) Domain bar. The colored bars immediately below the Chain bar indicate the locations of structural domains found by the original MMDB processing of the protein. In many cases, such a domain contains unconnected sections of the protein sequence, and in such cases, discontinuous pieces making up the domain will have bars of the same color. To the left of the Domain bar is a 3D Domains hyperlink (3d Domains) that launches the 3D Domains browser in Entrez, where the user can find information about each constituent domain. Selecting a colored segment displays the VAST Structure Neighbors page for that domain. (c) The CD bar. Below the VAST Domain bar are rounded, rectangular bars representing conserved domains found by a CD-Search. The bars identify the best scoring hits; overlapping hits are shown only if the mutual overlap with hits having better scores is less than 50%. The CDs hyperlink to the left of the bar displays the CD records in Entrez Domains. Each of the colored bars is also a hyperlink that displays the corresponding CD Summary page configured to show the multiple alignment of the protein sequence with members of the selected CD.

From: Chapter 3, Macromolecular Structure Databases

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The NCBI Handbook [Internet].
McEntyre J, Ostell J, editors.
Bethesda (MD): National Center for Biotechnology Information (US); 2002-.

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