Would it be possible for the PDB to explain the distinction in
representation between the case of a modified amino acid and the case of
additional atoms bound to the side chain of a standard amino acid. If
it is a standard amino acid will the extra atom(s) always be represented
as a het group? Is the PDB consistent through all entries in such a
case?
Frances Bernstein
On 2024-06-24 11:03, Marcus Bage wrote:
Hi everyone,
Last year wwPDB standardised the backbone atom names for all residues
that are part of a polypeptide sequence within the PDB archive. A full
list of all chemical components affected can be found at:
github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard
peptide residues within the PDB archive. It was last updated in August
2023.
wwPDB is in the process of standardising and enriching all protein
modification data in the PDB archive. As part of this, all modified
peptide residues will have data added to their CCD definition file to
describe in what way the residue is modified. For example, the 3-letter
code SEP, will have the information to state that it is the
phosphorylation of serine. Once this information is released it will be
considerably easier to access such information in the archive.
A detailed description of the changes being made as part of the PTM
standardisation project can be found at:
github.com/wwPDB/protein-modification-extension
Kind regards,
Marcus
On 24/06/2024 15:21, Harry Powell wrote:
Hi folks
“Can of worms” is how this could be described!
From various different sources (many thanks Paul, Mitch, Robbie) I
have now managed to obtain (inter alia) lists of 31, 189, 863 and 916
modified amino acids - and there are other, longer (and possibly
shorter and equimetric [is that even a word?] lists that I could
create if I want to be more comprehensive! It’s certainly _possible_
that some of the members of an individual list are duplicates, but for
my current purposes these should suffice nearly all the time (and for
those cases where the list falls short, I would expect people to raise
the issue directly with me…)
Once more, I knew this would be the place to ask!
Harry
On 24 Jun 2024, at 13:40, Robbie Joosten <robbie_joos...@hotmail.com>
wrote:
Hi Harry,
A BSc student in our lab just had a look at this. Here is the list of
mappings pdb-redo uses:
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif
(second to last loop).
Cheers,
Robbie
pdb-redo-main/tools/pdb-redo-data.cif at trunk ·
PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to
PDB-REDO/pdb-redo-main development by creating an account on GitHub.
github.com
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Harry
Powell <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] List of 3-letter codes of modified amino acids
Hi
An internet search doesn’t yield an obvious list of these (I did find
a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but
the link included appears to be dead -
http://deposit.pdb.org/hetdictionary.txt).
I’m almost convinced that this has been asked here previously (if not
recently), but a quick search through ccp4bb postings has not
revealed it to me.
Can anyone help?
Harry
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