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What is Enzyme Classification?
Enzyme Classification (EC) is based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). The PDB assigns EC (Enzyme Commission) numbers to protein chains in structures according to the type of chemical reaction catalyzed, specific donors and receptors of chemical groups participating in the reactions etc., all based on information from UniProtKB, GenBank, KEGG or are author specifications. Note: The browser includes enzymes for which an EC number has been assigned.
Why browse by EC Classification?
The EC classification groups enzymes that perform the same or related enzymatic functions. You can use the EC browser to explore enzymes that have similar functions, shape of enzyme and/or arrangements of amino acids performing the enzyme reaction. It can also be used to identify and explore structures of enzymes that have similar functions but different shapes and/or mechanism of enzyme reaction.
How to use the EC browser?
Users can browse by an EC class name, by typing in a specific enzyme name, or EC number (partial or full) in the search box at the top of the page.
After locating the enzyme of interest in the EC browser tree view the number of polymer entities (proteins) included in this group. Clicking on the numbers listed next to the process name will launch a search for all polymer entities in the PDB that are associated with that EC class.
Search for structures of DNA polymerase, an enzyme responsible for copying genetic material to make new copies of DNA, can be done as follows:
- browse the tree for “Transferases” >> “Transferring phosphorus-containing groups” >> “Nucleotidyltransferases” and “DNA-directed DNA polymerase” OR
- search by typing DNA polymerase in the search box on the page and select from the options “DNA-directed DNA polymerase” or typing in the EC number (type 220.127.116.11)