Hello researchers.
I'm working with spike proteín from SARS-CoV 2 and i notice that i don't know to proper clean an crystallography structure from PDB.
For example, i openned the 7Y9Z archive and notice that have a lot of Oligosaccharides chains on it. How i know if this chains is important for the proteín or was added for the stability of the crystallography method?
Thanks for the help.
Is there a reference cited for the structure determination? There should be some explanation there as to whether that is the actual formula or if other substituents we're added to aid in crystallizing it
Dear Jean,
You have to read up a bit about protein structures and their post translational modifications (PT). One of the most important PT is glycosylation. Sugars present in the entry you cited are covalently attached to the protein so therefore they are biologically relevant. How? You need to study by reading up. Their importance is multifold but usually do not play any dominant role in protein stability (albeit it might, like in the antibodies).
In order to connect on the right note and try to answer your question you must define what you mean by cleaning. For molecular docking or any other modeling activity the sugars probably should be left intact. For modeling new variants the sugars can be just simply edited out in the text editor or in any available modeling program. But may mean something else by cleaning. Your question is not clear.
Bog
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