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resource for structural class of proteins

Is there any resource from which structural class of proteins using their uniprot ids can be retrieved????

sequence
• 3,174 views • link
written by RT!37 • RT!37

3 answers

Hi

You can do it in 2step.

  1. Map uniprot IDs to PDB Ids using IDmapping tool (http://www.uniprot.org/uploadlists/)
  2. Go PDB advanced search, input pdb ids comma separated, submit, then generate custom report where u can select SCOP IDS.

Results can be downloaded as excel file.

Also you can explore : REST services of PDBe (https://www.ebi.ac.uk/pdbe/api/doc/sifts.html) and PDB (http://www.rcsb.org/pdb/software/rest.do)

Let me know if this does not help.

Thanks

Priyabrata Panigrahi

Persistent LABS

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written by Persistent LABS Persistent LABS

Thanks Priyabrata !! The two step procedure is working...!!! Actually I am trying to get SCOP class using Uniprot Ids, but the downloaded excel file have SCOP Ids.

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written by RT!37 • RT!37

You can search the SCOPe database. Example - P06213.

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written by GenoMax GenoMax

Thanks genomax2 !!! Example helped me to understand that single Uniprot id can belong to more than 1 class !!!

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written by RT!37 • RT!37

Thanks Priyabrata...

Sample: Id retriving Input : A0A4Z3,A0A8M2,A0AT29,A0AT32,A0AT33,A0AV96,A0AVK6,A0AVT1,A0FGR8,A0FGR9,A0FKI7 output pdbs were submitted to Advanced search and Scop Ids mapped

Only Output: 2DIS A 131532 [8-103] A0AV96

SCOp Id 131532 : when mapped with parseable file ( as provided in link by you) Results is 131532 px d.58.7.1 d2disa1 2dis A:8-103 which means 131532 belongs to Alpha and beta proteins (a+b).

Single uniprot id can harbor folds belonging to multiple Class , therefore a protein will be annotated with multiple structural class.

Please correct me if I am misinterpreting the results.

....

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written by RT!37 • RT!37

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWERS should be used only for new answers to original question.

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written by GenoMax GenoMax

Thanks Priyabrata !!

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written by RT!37 • RT!37

Yes you are right d.58.7.1 means class label is d (a+b protein).

Also you are correct that a protein can have multiple functional domains and each functional domains can be made up of multiple structural folds. SCOP classifies proteins based on fold-similarity. Thus for a single protein, there can be many SCOP domains, thus can have multiple scop ids mapped.

In order to understand better you can explore few entries PDB under Annotation section. You will see several SCOP domains can be present for a single PDB entries.

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written by Persistent LABS Persistent LABS

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