For those who do not know, I worked on data processing for the PDB from
1974 to 1998 (entries 15 to ~9000) and we tried to be consistent in
representing small modifications to amino acids: modified amino acid vs.
standard amino acid plus het group. With the then lack of software
tools we struggled to remember whether we had encountered a similar case
before. And there is the additional issue to consider of how the
depositor views the modification and discusses it in their publications.
I am glad to know that the PDB will be standardizing the data
representation of these cases.
Frances
On 2024-06-24 12:11, Marcus Bage wrote:
Hi Frances,
This is one of the central issues being addressed as part of the
protein modifications project.
When the PDB archive is updated as part of the project rollout, all
protein modifications will be grouped into distinct categories of
modification. The category they fall in determines how they will be
handled throughout the archive.
In general, small, well-described protein modifications will be handled
as part of the modified amino acid group. For example phosphorylations,
methylations and acetylations.
Modifications that that are large, branched or that link multiple
protein residues will be handled as linked het groups. For example
carbohydrates, hemes, lipids and crosslinkers.
This approach will make it easier to ensure that all modification
groups are handled in a single consistent way throughout the archive. A
significant effort is being made to standardise protein modifications
in all existing entries to ensure that this will be the case for the
whole archive.
For more detailed information about this project please see:
github.com/wwPDB/protein-modification-extension
Kind Regards,
Marcus
On 24/06/2024 16:44, f...@marbuta.pair.com wrote:
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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