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Source Organism Bowser (NCBI)

Searches or browses for structures by source organism. The Source Organism Browser is a hierarchical representation of all organisms in the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/Taxonomy/). All organisms which have structures in the PDB are listed as active links in the browser. These organisms are the source of the individual naturally-occurring macromolecules. The PDB source organism assignment is based on author/UniProt specified mapping.

The Source Organism Browser permits the user to navigate through the taxonomy hierarchy to arrive at the subset of particular interest. The browser opens up the top level in the hierarchy. Clicking on the arrow/folder icons expands the respective nodes. Clicking on the name of the node will retrieve all PDB IDs assigned to that node.

Important: Make sure pop-ups are enabled in your browser (Click here to check).

Examples

  1. Search by scientific organism name

    Homo Sapiens

    Type Homo Sapiens in the text box and click the "Find in Tree" button. The source organism tree expands and Homo Sapiens is highlighted in gray. Mouse over Homo Sapiens to see how many PDB proteins or nucleic acids entities (unique chains within a structure) are from a human source. Click on Homo Sapiens to retrieve these structures. Note, the number of structures retrieved will be lower than the number of entities displayed in the source organism tree since a structure may contain multiple entities.

  2. Browse the source organism tree

    EUKARYOTA

    Mouse over the CELLULAR ORGANISM to see the number of protein or nucleic acid entities (unique chains) from cellular organisms. Expand CELLULAR ORGANIMS by clicking on the triangle. To see the distribution of structures in the three domains mouse over ARCHAEA, BACTERIA, and EUKARYOTA. Click on EUKARYOTA to retrieve structures from eukaryotic origin.