Hi Ian
Yes, I understand that this causes an issue. My suggestion is to take this off the CCP4BB list and initially discuss this amongst a smaller group as part of our protein modification remediation project. I will contact representatives of the major refinement programs (Refmac, Phenix, Buster) to start a discussion on the representation of modified amino acids. If anyone else would like to be involved in this discussion please contact me directly and I will add you do the discussion. Regards John From: Ian Tickle <ianj...@gmail.com> Sent: 25 April 2019 10:20 To: John Berrisford <j...@ebi.ac.uk> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] “Bound ligand” versus “modified residue” Hi John As Pavel already mentioned, the problem with the ligand covalently bonded to a standard residue is that the bond is likely to change the geometry of the residue for atoms that are completely part of the residue, not just the atoms involved in the link. In that case one would still need to give the (no longer) standard residue a different name (I use something like 'A01', 'A02' etc.) and copy most of the geometry from the standard entry, changing those near the covalent link as needed. Then obviously one must also describe the peptide links made by A01. Cheers -- Ian On Thu, 25 Apr 2019 at 09:48, John Berrisford <j...@ebi.ac.uk <mailto:j...@ebi.ac.uk> > wrote: Hi The wwPDB procedure on this is listed in the “modified amino acids and nucleotides” section of https://www.wwpdb.org/documentation/procedure#toc_2 However, we are aware of the inconsistency in the PDB archive of how these modifications are represented and that there are lots of ligands which disagree with this procedure. We are in the early planning stages of a remediation of the PDB archive specifically on this topic and will be reaching out to the community to discuss this issue and to present our plans at a later date. Regarding mmCIF representation The mmCIF format allows both representations. In the case of a modified residue the residue has a parent of a standard residue and the one letter code of the standard residue. For example: phosphoserine, SEP, this ligand has a standard parent of SER and a one letter code of S. http://pdbe.org/chem/sep So for example in PDB entry 1apm we have the following loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes ;GNAAAAKKG(SEP)EQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDK QKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFAEPHARFYAAQIVLTFEY LHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTW(TPO)LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMA AGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEA PFIPKFKGPGDTSNFDDYEEEEIRV(SEP)INEKCGKEFTEF ; ;GNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVV KLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFAEPHARFYAAQIVLTFEYLHSL DLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKG PGDTSNFDDYEEEEIRVSINEKCGKEFTEF Where we list both the one_letter_code which contains SEP and a canonical sequence which contains S. There is also TPO (phosphotheronine) in this example which has a canonical sequence of T. (We are also aware that there are a number of modified residues which are missing the one letter code for the standard parent and are currently in the process of correcting this issue.) In the other representation, where the modification is linked to a standard residue, the standard residue is listed in the sequence and the linkage between the standard residue and the modification is described in struct_conn. I hope this helps John From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Nigel Moriarty Sent: 24 April 2019 18:55 To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] “Bound ligand” versus “modified residue” The "CYS with" means that the main chain is restrained and treated the same as "normal" CYS. However, I'm not sure how the sequence should be handled in the file especially mmCIF. Maybe John Berrisford can comment. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov <mailto:nwmoria...@lbl.gov> Fax : 510-486-5909 Web : CCI.LBL.gov <http://CCI.LBL.gov> On Wed, Apr 24, 2019 at 10:27 AM Pavel Afonine <pafon...@gmail.com <mailto:pafon...@gmail.com> > wrote: Hi Ian, perhaps there are as many answers to this as many subscribers to this list, but personally "Cysteine with attachment" seems more logic and clear to me than calling the whole thing a different name. Although I would also understand arguments like if it is a CYS with an attachment it is not really CYS any more and perhaps should be called a unique name. From refinement viewpoint both a fine. Pavel On Wed, Apr 24, 2019 at 8:59 AM Ian Clifton <ian.clif...@chem.ox.ac.uk <mailto:ian.clif...@chem.ox.ac.uk> > wrote: Hello everyone, PDB structure 4qdu contains a “modified residue”, 30V. This is joined into the rest of the main chain by means of LINK records. In 5kwj, a similar type of modification is described as a cysteine with a side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just two clear examples we found to illustrate the question.) Is there any reason to prefer one of these approaches over the other? Does it just depend on what ligands are already in the PDB? Thanks, -- Ian Clifton ⚗ ℡: +44 1865 275677 Chemistry Research Laboratory ℻: +44 1865 285002 Oxford University 📧: ian.clif...@chem.ox.ac.uk <mailto:ian.clif...@chem.ox.ac.uk> Mansfield Road Oxford OX1 3TA UK ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
