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The antibody light chains can either be kappa or lambda types. I am searching homologous sequences on the RCSB PDB website. Is there a way to filter out these two types?

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The instructions are as follows.

  1. Go to the RCSB PDB Webite.
  2. Under the search bar, click Browse by Annotations.
  3. Click the blue tab labeled SCOP.
  4. Click the white arrow next to the folder titled All Beta Protiens.
  5. Click the white arrow next to the folder titled Immunoglobulin-like beta-sandwich (...).
  6. Click the white arrow next to the folder titled Immunoglobulins (Superfamily).

This is where it splits, based on your specific search.

For Light Chain, Constant Domain:

  1. Click the white arrow next to the folder titled C1 set domains (antibody constant domain-like).
  2. For Kappa Type, Click the folder (not the arrow) titled Immunoglobulin light chain kappa constant domain, CL-kappa.
  3. For Lambda Type, Click the folder (not the arrow) titled Immunoglobulin light chain lambda constant domain, CL-lambda.

For Light Chain, Variable Domain:

  1. Click the white arrow next to the folder titled V set domains (antibody variable domain-like).
  2. For Kappa Type, Click the folder (not the arrow) titled Immunoglobulin light chain kappa variable domain, VL-kappa (...).
  3. For Lambda Type, Click the folder (not the arrow) titled Immunoglobulin light chain lambda variable domain, VL-lambda (...).

This should get you to the list of proteins that you are looking for.

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    $\begingroup$ Very very helpful! Just to confirm, would it be possible that some antibody PDB are not fully annotated so not included in this search? $\endgroup$ – lanselibai Apr 1 '20 at 0:17
  • $\begingroup$ Yes, a lot of them are not included in the above searches. However, you can find most of the rest here -> rcsb.org/pdb/search/… $\endgroup$ – mpprogram6771 Apr 1 '20 at 0:23
  • $\begingroup$ @lanselibai Would you like me to add instructions for heavy chain types as well? $\endgroup$ – mpprogram6771 Apr 1 '20 at 13:48
  • $\begingroup$ Of course, go for it! $\endgroup$ – lanselibai Apr 2 '20 at 0:43

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