This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate synthase and the paper I referenced only as an example. But sadly, it's not a great example because the authors have not submitted their (predicted) model of the exact ligand configuration during the critical catalytic step when actually the Galactose is added at beta-configuration to the Glucose.

I would like to find another example which of an enzyme, perhaps involving a metal ion too, for which we have pretty exact configurations submitted to PDB that show how exactly the reactants are aligned to create a specific reaction with a specific stereo-configuration, so we can see why exactly the reaction occurs on that atom and in that direction.

I thought the glycolysis pathway should be very well understood by now, but when I went to UniProt KB looking for the hexokinase, I do not see any tertiary structure model with any ligand. Besides, the glycolysis is a catabolic pathway, and I'd like to show an anabolic reaction, although if I remember correctly, many of the glycolysis steps are reversible.

Appreciate if you can point me to better examples that have lots of "snapshots" of the reaction publicly available.

EDIT comment:

This is what I am looking for: an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactate synthase -- we have snapshots for the critical step of the reaction: the alignment of two ligands which get bonded into a single stereo-isomer. There is nothing dumb, nothing too broad, and nothing opinion-based about this question. The truth is, it's hard to find one by just trial and error fishing on PDB or UniProt.

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    $\begingroup$ How would you tell if something is best studied? $\endgroup$
    – Mithoron
    Sep 30, 2021 at 20:10
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    $\begingroup$ How do you define «best studied», what threshold(s) do you use to define «this is good enough»? Hunting for multiple X-ray snapshots of one reaction/type of reaction with enzymes reads like establishing a trajectory like Bürgi & Dunitz pioneered (the later recently embarked for his last way). So «Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches» by Westenhoff et al. in Acta Cryst. (2010) A66, 207–219 (doi 10.1107/S0108767309054361, open access) may offer an entry about these bigger molecules. $\endgroup$
    – Buttonwood
    Sep 30, 2021 at 21:01
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    $\begingroup$ Do people get crystal structures of the enzyme bound to its actual substrate? I was under the impression that it's easier to get the structure of a complex with a competitive inhibitor. $\endgroup$ Oct 1, 2021 at 17:40
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    $\begingroup$ @GuntherSchadow - I have added a comment on your other question. The comments here are not intended to be negative, they are intended to get to the heart of the matter within the site's guidelines. $\endgroup$ Oct 1, 2021 at 18:31
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    $\begingroup$ Following up on @orthocresol , it is very difficult to determine structures of wild-type enzymes with substrates except at cryo temperatures because the substrates react to products more quickly than any structural data collection method. More often you will see structures with inhibitors that mimic the proposed transition state or substrates bound to inactive variants of the enzyme. Some people generate computational models of the substrate in the wild-type active site and maybe even simulate the reaction, but those structures/simulations don't go to PDB usually. $\endgroup$
    – Andrew
    Oct 1, 2021 at 18:34


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