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 <[email protected]>
To: [email protected]
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."
