Atom and residue nomenclature has been standardized in a variety of ways in PDB version 3.0 data files. All changes in nomenclature are documented in the electronic chemical components dictionary.
The changes in nomenclature include:
- IUPAC nomenclature for standard amino acid and nucleotides. Atoms names follow the recommendations of described in Pure & Appl. Chem., 70, 117-142, 1998. with the exception of the well-established convention for C-terminal atoms OXT and HXT. In this and other cases where an atom name has been changed, the previous name is retained in an alternate name in the PDB Chemical Components dictionary.
- Discrimination of DNA and RNA linking nucleotides and modifications. Deoxy- and ribose nucleotides now have separate chemical definitions with the DNA forms relabeled as DA, DC, DG, DT, DI and DU. Modified nucleotides formerly identified as using plus- syntax (e.g. +C, +G) have been relabeled with the particular 3-letter code corresponding to the full chemical description of the modified nucleotide.
More conventional atom labeling for non-polymer atoms.
In the new chemical definitions the following changes have been made to move the atom naming to a more conventional state.
- Atom names begin with their element symbol.
- Heavy atom names follow the traditional PDB justification rules in which the atom element symbol is right justified in the second character position of the 4-character atom name. 4-character names for atoms with 1-character element symbols have been compressed to 3 characters.
- Hydrogen atoms names all begin and are not subject to the justification rule.
- Removal of redundant and deprecated ligands. In cases where the same monomer or ligand had been defined using different identifiers, the most common identifier has been retained and the others have been marked as obsolete. Definitions which were deemed incorrect or better represented in other ways (e.g. metal hydrates) have also been obsoleted.
© 2007 wwPDB