Dear colleagues, We deposited protein structures with modified lysine side chains and were surprised that the PDB treats the modification as an independent molecule, with a “LINK” record indicating the covalent bond – instead of defining a modified residue (that’s what we had uploaded to the PDB). Apparently, anything attached to an amino acid is considered an independent molecule (and the lysine just called a regular lysine) if it comprises more than 10 atoms (see below for the PDB guidelines).
I think that’s kind of arbitrary and would give all modified residue also modified names – i.e. individual names for all modified lysines, as it is done for acetyl- or methyl-lysines, for example. I wonder what other people’s opinion is?! Best regards Clemens ------------------------------------------------------------------------------------------------ This is in accordance to the wwPDB annotation guidelines (http://www.wwpdb.org/procedure.html#toc_2). "*Modified amino acids and nucleotides* If an amino acid or nucleotide is modified by a chemical group greater than 10 atoms, the residue will be split into two groups: the amino acid/nucleotide group and the modification. A link record will be generated between the amino acid/nucleotide group and the modification. For modified amino acids and nucleotides that were not split will follow standard atom nomenclature."
