Hi folks Another quick update - I am also parsing mmCIF (and also associated JSON) files from PDB - so if there are ligands in those files that I can identify unambiguously as being associated with *only one chain* (this is very important to me…), then I’ll include these as “ligands” in my studies, but not as cofactors *unless* they appear as cofactors in UniProt.
A person has to know their limitations… to paraphrase another Harry. Harry > On 20 Dec 2024, at 12:11, Harry Powell > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi folks > > Before anyone points this out, I notice from PDB 2BS2 (I’ve only looked on > PDBe for this, RCSB and PDBj might differ in their “added value annotation"!) > and UniProt P17596 that one calls iron-sulfur clusters “ligands” and the > other calls them “cofactors”. > > For my current purposes, I’m using the UniProt nomenclature because I’m > parsing files from them. I’ll worry about what’s _really_ a cofactor at a > later date! > > Best wishes > > Harry > >> On 20 Dec 2024, at 11:47, Harry Powell <hrp-ccp...@virginmedia.com> wrote: >> >> Wow. I was right about one thing - this _is_ a good place to ask. >> >> Many thanks for the flood of responses - that will keep me busy for a while >> - I’ll get back to you with what I think are the most useful ones for my >> purposes (so many, many apologies to those people who have taken the time to >> respond but came up with suggestions that didn’t "hit the spot" for some >> reason!). >> >> Just for the record, I’m not interested in any co-factors like water or >> “isolated” metal ions (so not part of a bigger assembly - I’m interested in >> things like haem, for example, but not things like hexaaquacobalt). So >> anything that has (say) FAD and ADP bound by the same chain would pique my >> interest - especially if both are listed in the corresponding UniProt KB >> entry (just because a PDB entry has more than one ligand bound, they may not >> both really be cofactors…). If UniProt KB tells me that there’s only one >> cofactor (or worse, none), then I will rapidly move on (unless someone can >> provide a solid justification as to why UniProt is wrong and they’re right…). >> >> Enjoy a solstice-oriented break! >> >> best wishes >> >> Harry >> >>> On 20 Dec 2024, at 10:37, Harry Powell >>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> Hi folks >>> >>> I’m familiar with enzymes that have a single co-factor (for example haem in >>> myoglobin [or in the individual chains in haemoglobins] or FAD in >>> flavoproteins), but was wondering if there are examples of single-chain >>> proteins that have multiple cofactors (or even multiple chain proteins that >>> have multiple cofactors bound to a single chain)? >>> >>> I’m not bothered (at the moment) about proteins that have cofactors bound >>> to different chains. >>> >>> I thought this would be a good place to ask… >>> >>> Harry >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >>> https://www.jiscmail.ac.uk/policyandsecurity/ >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
