<p>Tried looking for an explicit database? i.e.</p>

<ul>
<li>ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808974/" rel="noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808974/</a> or</li>
<li>LigASite: a database of biologically relevant binding sites in proteins with known apo-structures <a href="https://www.ncbi.nlm.nih.gov/pubmed/17933762" rel="noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/17933762</a></li>
</ul>

<p>Else the PDB itself has a very powerful advanced search that should allow you to do this: <a href="http://www.rcsb.org/pdb/search/advSearch.do" rel="noreferrer">http://www.rcsb.org/pdb/search/advSearch.do</a></p>

CC BY-SA 3.0
2017-06-21T13:36:08.693Z
2017-06-21T13:36:08.693Z
Dan
<p>Are you aware of <a href="http://www.brenda-enzymes.org/index.php" rel="nofollow noreferrer">BRENDA</a>? I was just introduced to it today for a completely separate reason (looking at carbohydrate enzyme families in the <em>Nippostrongylus brasiliensis</em> proteome), and it seems to be a fairly comprehensive database. There is at least a literature link there for the <a href="http://www.brenda-enzymes.org/enzyme.php?ecno=1.11.1.11#Crystallization/COMMENTARY" rel="nofollow noreferrer">ascorbate-complexed crystalisation of Ascorbate peroxidase</a> on that site. Following through the paper, I see that <a href="http://www.rcsb.org/pdb/explore/explore.do?pdbId=1OAF" rel="nofollow noreferrer">the complex has been uploaded to PDB</a>.</p>

CC BY-SA 3.0
2017-06-13T04:45:30.723Z
2017-06-13T04:45:30.723Z
gringer
<p>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 </p>

<ul>
<li>Ascorbate peroxidase (APX)</li>
<li>Beta-glucosidase</li>
<li>Calcineurin b-like protein-interacting protein kinase.</li>
</ul>

<p>I've searched in PDB and UNIPROT. </p>

CC BY-SA 3.0
2017-06-13T04:38:41.370Z
Hi Lock23, thanks for your question and welcome to Bioinformatics Stack Exchange. After reading your question, I did a quick check on the [Biology](https://biology.stackexchange.com/search?q=enzyme+database) and [Chemistry](https://chemistry.stackexchange.com/search?q=enzyme+database) Stack Exchanges, and was surprised at how little "database" stuff there was.
gringer
CC BY-SA 3.0
2017-06-13T08:33:47.200Z
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).
marcin
<database><protein-structure>
how to find the bound form of an enzyme structure?
# how to find the bound form of an enzyme structure?

(Asked by: username_0 on 2017-06-13)

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.

**Tags:** database, protein-structure
> **Comments:**
> **username_1**: Hi Lock23, thanks for your question and welcome to Bioinformatics Stack Exchange. After reading your question, I did a quick check on the [Biology](https://biology.stackexchange.com/search?q=enzyme+database) and [Chemistry](https://chemistry.stackexchange.com/search?q=enzyme+database) Stack Exchanges, and was surprised at how little "database" stuff there was.  
> **username_2**: 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).  

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## 2 answers

### Answer by username_3 on 2017-06-21. Score: 5

Tried looking for an explicit database? i.e.

* ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808974/> or
* LigASite: a database of biologically relevant binding sites in proteins with known apo-structures <https://www.ncbi.nlm.nih.gov/pubmed/17933762>

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>


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### Answer by username_1 on 2017-06-13. Score: 4

Are you aware of [BRENDA](http://www.brenda-enzymes.org/index.php)? 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](http://www.brenda-enzymes.org/enzyme.php?ecno=1.11.1.11#Crystallization/COMMENTARY) on that site. Following through the paper, I see that [the complex has been uploaded to PDB](http://www.rcsb.org/pdb/explore/explore.do?pdbId=1OAF).


---

