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
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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."
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