For my undergraduate research I'm looking for a database that gives the bound form of a particular protein structure. Is there any database that provide us with such data? So far I've found following proteins related to my work

  • Ascorbate peroxidase (APX)
  • Beta-glucosidase
  • Calcineurin b-like protein-interacting protein kinase.

I've searched in PDB and UNIPROT.

  • $\begingroup$ Hi Lock23, thanks for your question and welcome to Bioinformatics Stack Exchange. After reading your question, I did a quick check on the Biology and Chemistry Stack Exchanges, and was surprised at how little "database" stuff there was. $\endgroup$ – gringer Jun 13 '17 at 4:38
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    $\begingroup$ For experimentally determined structures PDB is the database and it's unlikely you'll find structures that are publicly available but not in the PDB. There is also protein structure prediction software (servers). $\endgroup$ – marcin Jun 13 '17 at 8:33

Tried looking for an explicit database? i.e.

Else the PDB itself has a very powerful advanced search that should allow you to do this: http://www.rcsb.org/pdb/search/advSearch.do


Are you aware of BRENDA? I was just introduced to it today for a completely separate reason (looking at carbohydrate enzyme families in the Nippostrongylus brasiliensis proteome), and it seems to be a fairly comprehensive database. There is at least a literature link there for the ascorbate-complexed crystalisation of Ascorbate peroxidase on that site. Following through the paper, I see that the complex has been uploaded to PDB.


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