Answers.Body: <p><a href="https://www.rcsb.org/structure/15C8" rel="nofollow noreferrer">PDB structure 15C8</a> corresponds to the protein product of the mouse <em>Igkc</em> gene, with the UniProt accession <a href="https://www.uniprot.org/uniprot/P01837" rel="nofollow noreferrer">P01837</a> as you can see in the linked page:</p>
  <p><a href="https://i.sstatic.net/rfTlX.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/rfTlX.png" alt="screenshot of PDB entry 15C8" /></a></p>
  <p>Your <a href="https://www.uniprot.org/uniprot/P01869" rel="nofollow noreferrer">P01869</a> UniProt accession is for the protein product of the mouse <em>Ighg1</em> gene instead, so why would you expect these to be the same sequence? They are different proteins coded for by different genes.</p>
  
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Answers.Text: Thanks for your response! I got the P01869 after looking it up in this tool: https://www.uniprot.org/uploadlists/ (from PDB to UniProtKB). This returns both P01837 and P01869 -- do you happen to understand why?
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Answers.Text: 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
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Answers.Text: @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.
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Body: <p>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:</p>
  <pre><code>DIVLTQSPAIMSASLGERVTMTCTASSSVSSSNLHWYQQKPGSSPKLWIYSTSNLA
  SGVPARFSGSGSGTSYSLTISSMEAEDAATYYCHQYHRSPYTFGGGTKLEIKRADA
  APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQD
  SKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN
  </code></pre>
  <p>and</p>
  <pre><code>EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQKPEQGLEWIAQIDPANG
  NTKYDPKFQGKATITADTSSNTAYLHLSSLTSEDSAVYYCAADPPYYGHGDYWGQG
  TTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSG
  VHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIV
  </code></pre>
  <p>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: <a href="https://www.uniprot.org/uniprot/P01869" rel="nofollow noreferrer">https://www.uniprot.org/uniprot/P01869</a>). However, looking at the AlphaFold entry, I see that the amino acid sequence looks different, eg. for the case above it's:</p>
  <pre><code>AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAV
  LQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVP
  EVSSVFIFPPKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVHTAQTQP
  REEQFNSTFRSVSELPIMHQDWLNGKEFKCRVNSAAFPAPIEKTISKTKGRPKAPQ
  VYTIPPPKEQMAKDKVSLTCMITDFFPEDITVEWQWNGQPAENYKNTQPIMNTNGS
  YFVYSKLNVQKSNWEAGNTFTCSVLHEGLHNHHTEKSLSHSPGLQLDETCAEAQDG
  ELDGLWTTITIFISLFLLSVCYSAAVTLFKVKWIFSSVVELKQTLVPEYKNMIGQA
  P
  </code></pre>
  <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?</p>
  
Tags: <proteins><protein-structure><pdb><uniprot>
Title: Relationship between entries for same UniProt Id
ThreadText: # Relationship between entries for same UniProt Id
  
  (Asked by: username_0 on 2022-02-10)
  
  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?
  
  **Tags:** proteins, protein-structure, pdb, uniprot
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-02-10. Score: 1
  
  [PDB structure 15C8](https://www.rcsb.org/structure/15C8) corresponds to the protein product of the mouse *Igkc* gene, with the UniProt accession [P01837](https://www.uniprot.org/uniprot/P01837) as you can see in the linked page:
  
  [![screenshot of PDB entry 15C8](https://i.sstatic.net/rfTlX.png)](https://i.sstatic.net/rfTlX.png)
  
  Your [P01869](https://www.uniprot.org/uniprot/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.
  
  > **Comments:**
  > **username_0**: Thanks for your response! I got the P01869 after looking it up in this tool: https://www.uniprot.org/uploadlists/ (from PDB to UniProtKB). This returns both P01837 and P01869 -- do you happen to understand why?  
  > **username_0**: 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  
  > **username_1**: @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.  
  
  ---
  
  