Data Uniformity and Enzyme Classification

In the PDB's on-going effort to improve the reliability of searches, the data uniformity project looked at the accurate query of enzymes according to the Enzyme Commission classification, including the EC number and name. The enzyme classification was derived directly from the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). The PDB would like to acknowledge the work of Dietmar Schomburg of the Institute of Biochemistry at the University of Cologne, and Project leader of the BRENDA database for enzyme classification remediation.

EC numbers were extracted from the PDB files either from the PDB Compound (COMPND) records or by a text search of the PDB file. A relational table associating EC number with compound name was constructed for all PDB enzyme entries. This table was then used along with the nomenclature used by the Enzyme Commission to search by compound name and identify the missing EC numbers. A manual verification of all the data was used to make the final EC assignments in the database. A description of query and reporting on EC numbers is available at http://www.rcsb.org/pdb/newsletter/2000q3/new_query.html.