- really the only complicated case would be where a group is covalently linked to more than one amino acid, wouldn't it? Any case where only one covalent link with an is present could (should?) be treated as a special amino acid, i.e. like selenomethionine.
- groups without any covalent links to the protein are better kept separate I would think (but I guess this is stating the obvious).
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaijOn 9 Jul 2013, at 12:49, Frances C.
Bernstein wrote:
> In trying to formulate a suggested policy on het groups
> versus modified side chains one needs to think about the
> various cases that have arisen.
>
> Perhaps the earliest one I can think of is a heme group.
> One could view it as a very large decoration on a side
> chain but, as everyone knows, one heme group makes four
> links to residues. In the early days of the PDB we decided
> that heme "obviously" had to be represented as a separate group.
>
> I would also point out that nobody would seriously suggest that
> selenomethionine should be represented as a methionine with a
> missing sulfur and a selenium het group bound to it.
>
> Unfortunately all the cases that fall between selenomethionine
> and heme are more difficult. Perhaps the best that one must
> hope for is that whichever representation is chosen for
a
> particular case, it be consistent across all entries.
>
> Frances
>
> P.S. One can also have similar discussions about the representation
> of microheterogeneity and of sugar chains but we should leave those
> for another day.
>
> =====================================================
> **** Bernstein + Sons
> * * Information Systems Consultants
> **** 5 Brewster Lane, Bellport, NY 11713-2803
> * * ***
> **** * Frances C. Bernstein
> * ***
[log in to unmask]> ***
*
> * *** 1-631-286-1339 FAX: 1-631-286-1999
> =====================================================
>
> On Tue, 9 Jul 2013, MARTYN SYMMONS wrote:
>
>> 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 <
[log in to unmask]>
>> To:
[log in to unmask]>> 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."