Hi Clemens I guess the reason you say 'arbitrary' is because there is no explanation of this rule decision? It would be nice if some rationalization was available alongside the values given. So a sentence along the lines of 'we set the number owing to the following considerations' ?
However a further layer of variation is that the rule does not seem to be consistently applied - just browsing CYS modifications: iodoacetamide treatment gives a CYS with only 4 additional atoms but it is split off as ACM. However some ligands much larger than 10 residues have been kept with the cysteine ( for example CY7 in 2jiv and NPH in 1a18. My betting is that it depends on whether something has been seen 'going solo' as a non-covalent ligand previously so that it pops up as an atomic structural match with a pre-defined three-letter code. This would explain for example the ACM case which you might expect to occur in a modified Cys. But it has also been observed as a non-polymer ligand in its own right so goes on as a separate modification? However to be honest I am not sure I have ever seen the rationale for this written down. 'Non-polymer' heterogens can turn up either linked or not. Once they are in the residues they have to make a call on which kind of backbone they will feature in within the pdb. That is why there is 'D5M' for non-polymer deoxyAMP. Also known as ' DA' when it is 'DNA-linking' but so far not fessing up to life under a third code as 'RNA-linking'.... Now is perhaps the time to ask for explanations of these nomenclature features before they become hard-wired in the new pdb deposition system (however there may be time - I refer you to my previous posting ;). Cheers Martyn Dr Martyn Symmons Cambridge ________________________________ From: Michael Weyand <michael.wey...@uni-bayreuth.de> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 8 July 2013, 10:03 Subject: [ccp4bb] modified amino acids in the PDB 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."
