Does the protein structure shown in the JSmol link have any Sulfur Dioxide molecules?
In the picture, the Sulfur element is yellow and Oxygen is red (see here)
Link to mmcif file (I have the VS Code plugin installed):
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The answer, as provided in the comments by gilleain is No. The commenter wanted to know why I asked this. The reason is I heard sulfur dioxide as silent speech when thinking about antibodies that’s why I asked.
I searched the file https://files.rcsb.org/view/1P9S.cif for the SO2 molecule and didn't find it. I got confirmation in the comments of the question.
Would anyone be interested in an app that takes a .cif file of a molecule and allows you to search the file for any type of element or molecule in it? Would that help anyone with their research?
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1$\begingroup$ Sorry, I do not see the advantage. All three PDB databases allow ligand search by name, residue name or SMILES in the browser. The PDBe has a decent API (ebi.ac.uk/pdbe/pdbe-rest-api), which gives info of which ligands are present, without downloading the structure. Furthermore, most instances of elements beyond the 6 of life are crystallisation artefacts, so it is way safer to search for enzymes that are expected to have more exotic elements, e.g. tungsten in a W-enzyme as seen in PDB:2W7Z. $\endgroup$ Commented Jun 7, 2021 at 8:59