POP-OUT | CLOSE

PDB Focus: Enzyme Queries Using SearchFields

Enzymes in the PDB have been classified in a hierarchical tree structure using the standards of the Enzyme Commission (EC). This classification permits users to search for enzymes by EC number or EC class/name through the SearchFields interface. It also allows users to "browse" through all enzymes using an Enzyme Browser interface, also available through SearchFields.

EC searches can be accomplished by selecting the "EC Number and Classification" option at the bottom of the SearchFields form, and then pressing the "New Form" button. New fields for "EC Number" and "Enzyme Class/Name" will then be available for searches based on these parameters. For example, searches for HIV-1 Protease in the PDB can be performed by entering "Retropepsin" in the "Enzyme Class/Name" field or by entering "3.4.23.16" in the "EC Number" field.

Selecting the "Browse and Select from Enzyme Classification" link under the "Enzyme Class/Name" box will launch the Enzyme Browser in a separate window. This interface allows users to navigate through different echelons of enzyme classification to arrive at a subset of particular interest. In the Enzyme Browser table, clicking on the "EC Number" column allows you to move up and down the EC tree. Clicking on a number in the "# of Structures in the PDB" column item gives you access to all those structures in the "Query Result Browser". Selecting the "use" link for any row will bring that EC Number and Enzyme Class/Name into the query form so that you can search the PDB database for that specific item.

The enzyme name/classification can be used only with the nomenclature or subclass exactly as given in the Enzyme Commission Nomenclature or substrings thereof.

Enzyme Nomenclature (1992) Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Academic Press, New York.

Related information is available at the following Web sites:

http://www.chem.qmw.ac.uk/iubmb/
http://www.genome.ad.jp/
http://www.expasy.ch/enzyme/
http://www.rrz.uni-hamburg.de/biologie/b_online/d18_1/ec.htm

Further details on using this feature can be accessed at http://www.rcsb.org/pdb/query_tut.html.