Dear Marc (and BB),

I guess as usual, in real life the obvious is less obvious as it seems to be. I, and I guess many of my colleagues trying to find new drugs, have quite a few protein-inhibitor complexes where the inhibitor formed a covalent link with e.g. the active site serine. In these cases, I am perfectly happy with having the inhibitor being defined as a separate group, linked via a LINK record. For me, it does not make sense to treat these covalent inhibitors differently from noncovalent inhibitors.

In the end, I guess, it will boil down to some arbitrary choice, either imposed upon us by the pdb, or individually taken by the crystallographer who produced the crystal structure.

My 2 cts,
Herman
 

-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Mark J van Raaij
Gesendet: Dienstag, 9. Juli 2013 16:23
An: [log in to unmask]
Betreff: Re: [ccp4bb] modified amino acids in the PDB

- 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/~mjvanraaij





On 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.
> 
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> 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."