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How can one find the information of a protein environment ph from its PDB id? Can one assume the ph to be the same as its cellular location?

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I know that ENSEMBL, PDB and the Human Atlas give known locations for many proteins at different levels of certainty, but such data is far from complete. Also experimental indication of a proteins localization does not prove the absence at other locations. Dependent on your scientific questions it might still be valid to theoretically look into specific scenarios of a proteins localization and to assume a certain pH of that sub-cellular context. SO to answer your question: Higher pH-resolution than the hypothesized cellular sub-localization is unrealistic, and the justification of the assumption of localization depends on your specific plan.

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  • $\begingroup$ So can one assume that a protein uniprot.org/uniprot/O96693 located in the apicoplast will function at that ph (the one of the apicoplast)? $\endgroup$ – BND Aug 21 '20 at 17:26
  • $\begingroup$ I am not saying that it is correct to make that assumption, but that high-resolution pH estimates seem unrealistic to me, as you clearly don't have enough information, as you wouldn't ask the question if you did. For me your assumption of taking the pH of the known compartment seems to be the least problematic one, out of all options. Only you can make that call in the end. $\endgroup$ – KaPy3141 Aug 21 '20 at 20:38

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