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biotite-dev / hydride

Adding hydrogens to molecular models
https://hydride.biotite-python.org/
BSD 3-Clause "New" or "Revised" License
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Peptide bond is not detected #22

Closed dargen3 closed 2 days ago

dargen3 commented 1 week ago

Hello,

I'd like to report a probable bug. I used a structure from the PDB with the code 2JT9. The hydride version is 1.2.3. When I protonate the structure using hydride (hydride --infile 2jt9.cif --outfile protonated.cif), the oxygen and carbon in the peptide bond between ACA7 and ARG8 are protonated incorrectly. It looks as if the double bond between oxygen and carbon is not recognised and therefore hydrogens are added to both atoms.

image

padix-key commented 1 week ago

You are quite good in finding structures with edge cases I have not encountered before :+1:. In this case however, I would put the blame on the structure itself:

The culprit here is the oxygen atom. Instead of the O atom as used normally in a peptide, the oxygen is named OXT. In the 'Chemical Component Dictionary' OXT (in contrast to O) is only single-bonded, i.e. a hydroxy group. Therefore, the hydrogen atoms at the carbon and the oxygen are actually correct, the problem is the wrong annotation in the structure file. When you look at your posted image, you see that PyMOL also detects the oxygen as single-bonded hydroxy group. This is also true for Mol* (https://www.rcsb.org/3d-view/2JT9).

dargen3 commented 6 days ago

Thank you! :smile: And thank you for the explanation. It makes sense. It never stops surprising me what everything can go wrong in PDB...