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I have 2 questions regarding the naming of secondary structure elements ($\alpha$-helix and $\beta$-sheets), like helix C or sheet 2, which are often used in publications.

Example protein: CYP1A2

PDB code: 2HI4

DOI of publication: 10.2210/pdb2HI4/pdb

Now my questions:

  1. Who assigns the characters and numbers to the helices and sheets? The authors of the paper where the structure is published (considering possible homologues or canonical folds)? Some institution?
  2. Is there a database/website where one can easily look up the right naming? I could not find any such information on RCSB webpage's entries. Or is it always necessary to look at the publication?

I read that there would be a 'canonical P450 fold' - but I could not find any naming conventions.

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  • $\begingroup$ Could you clarify. Where are you reading this information? Am I right in assuming that it is the Protein Databank web pages at RCSB. If so, I imagine that they have a submission form for authors to enter details, but I am sure they put the structure and sequence through a series of programs to assign secondary structure and motifs. As for where ‘canonical P450 fold’ is referenced, you should write and ask. They have the resources to answer queries. $\endgroup$ – David Feb 5 at 22:26

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