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
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