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I was playing around, looking at some AlphaFold predictions for certain proteins and I realized that sometimes the sequences of aminoacid look very different for the same UniProt id. For example, 15C8 from PDB has 2 chains:

DIVLTQSPAIMSASLGERVTMTCTASSSVSSSNLHWYQQKPGSSPKLWIYSTSNLA
SGVPARFSGSGSGTSYSLTISSMEAEDAATYYCHQYHRSPYTFGGGTKLEIKRADA
APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQD
SKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

and

EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQKPEQGLEWIAQIDPANG
NTKYDPKFQGKATITADTSSNTAYLHLSSLTSEDSAVYYCAADPPYYGHGDYWGQG
TTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSG
VHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIV

At the same time, when looking at the UniProt database (the corresponding id is P01869), there's a list of multiple structures and their 3D shapes (here: https://www.uniprot.org/uniprot/P01869). However, looking at the AlphaFold entry, I see that the amino acid sequence looks different, eg. for the case above it's:

AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAV
LQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVP
EVSSVFIFPPKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVHTAQTQP
REEQFNSTFRSVSELPIMHQDWLNGKEFKCRVNSAAFPAPIEKTISKTKGRPKAPQ
VYTIPPPKEQMAKDKVSLTCMITDFFPEDITVEWQWNGQPAENYKNTQPIMNTNGS
YFVYSKLNVQKSNWEAGNTFTCSVLHEGLHNHHTEKSLSHSPGLQLDETCAEAQDG
ELDGLWTTITIFISLFLLSVCYSAAVTLFKVKWIFSSVVELKQTLVPEYKNMIGQA
P

My question (as someone who's just getting started with proteins) would be: what is the relationship between all these entries corresponding to the same UniProt Id?

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PDB structure 15C8 corresponds to the protein product of the mouse Igkc gene, with the UniProt accession P01837 as you can see in the linked page:

screenshot of PDB entry 15C8

Your P01869 UniProt accession is for the protein product of the mouse Ighg1 gene instead, so why would you expect these to be the same sequence? They are different proteins coded for by different genes.

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  • $\begingroup$ Thanks for your response! I got the P01869 after looking it up in this tool: uniprot.org/uploadlists (from PDB to UniProtKB). This returns both P01837 and P01869 -- do you happen to understand why? $\endgroup$
    – CubeHead
    Feb 10, 2022 at 18:03
  • $\begingroup$ And in any case, my confusion regarding the amino acid sequence still holds using the correct UniProt id you mentioned, as AlphaFold has the following sequence: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC which is a substring of the first chain in my original post + "EC" at the end $\endgroup$
    – CubeHead
    Feb 10, 2022 at 18:05
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    $\begingroup$ @Andreea that's... a different question but yes, the structure predictions of AlphaFold or SwissFold or any other such collection tend to be of only parts of a protein and not the entire thing. As for why you got both, that's because P01837 and P01869 are similar proteins and the specific sub-sequence whose structure has been predicted occurs in both of them. $\endgroup$
    – terdon
    Feb 10, 2022 at 18:21

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