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In the PDB data file format for macromolecular models, each atom is designated either ATOM or HETATM (which stands for hetero atom). ATOM is reserved for atoms in standard residues of protein, DNA or RNA. HETATM is applied to non-standard residues of protein, DNA or RNA, as well as atoms in other kinds of groups, such as carbohydrates, substrates, ligands, solvent, and metal ions.
At PDB.Org, using the Advanced Search and query type Chemical ID, you can find all entries in the database that contain a particular chemical component. For example, in March, 2010, five entries contain PYL (explained in Non-Standard Residues).
A complete list of all compounds in the PDB is available, including hydrogens, 3D structures, and bond orders, in the Chemical Components Dictionary of the Worldwide Protein Data Bank. This includes all Standard Residues as well as Non-Standard Residues, carbohydrate adducts, Ligands and Hetero Groups. It is updated weekly for newly released entries.