How are three-letter residue names and chain identifiers for residue modifications and ligands assigned?
A. There are four common cases: covalently bound ligands, protein residue modifications, nucleotide modifications, metal coordination interactions (for example the interaction between iron and histidine in hemoglobin), and non-covalently bound ligands. Covalently bound ligands: A traditional distinction has been made between covalently bound ligands and small residue modifications. A bound ligand is defined as a modification with greater than 10 atoms including hydrogens. Covalently bound ligands are assigned the chain identifier of the polymer chain to which the ligand is bound. The bonding between the ligand and the residue is specified in PDB LINK records. The ligand coordinates appear as HETATM records following either the TER record for the bound chain or after the TER record for the last polymer chain. The ligand is assigned a unique residue number within chain to which it is bound. The residue that binds the ligand retains its standard name in both coordinate and SEQRES records.
