Standard Residues
Standard residues (standard amino acids and nucleotides) are defined in the PDB data file format, and have record type ATOM in PDB-format atomic coordinate files. Standard residues are:
- The 20 standard amino acids, plus ambiguous residue codes ASX, GLX, and undetermined UNK.
- Twelve standard nucleotides A, C, G, I, T, U, DA, DC, DG, DI, DT, and DU plus UNK.
The distinction between ribonucleotides (A, C, G, I, T, 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".
See also