- The 20 standard amino acids, plus ambiguous residue codes ASX, GLX, and undetermined UNK. In 2014, the PDB is in the process of adding SEC (U) and PYL (O) making 22 standard amino acids.
- Eleven standard nucleotides A, C, G, I, U, DA, DC, DG, DI, DT, and DU, plus N for an unknown nucleotide. (I is inosine.) The PDB provides this list under HET.
The distinction between ribonucleotides (A, C, G, I, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU) was first made when the PDB was remediated, effective August 1, 2007. The unremediated files can still be obtained, see Getting Unremediated PDB Files.
Note that, in Jmol, A, C, G, I, T, U select nucleotides in either DNA or RNA for backward compatibility, while DA, DC, DG, DI, DT, and DU select only DNA nucleotides. You can select RNA nucleotides with e.g. "(A, U) and RNA", or by enclosing the single-letter nucleotide names in brackets, e.g. "([A],[C],[G],[I],[U])".
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.