<p>In cases when you cannot find answer through the web interface, you can <a href="http://www.wwpdb.org/download/downloads" rel="nofollow noreferrer">download all the data</a> and search it locally.</p>

<p>Relying on the PDB annotations of SS bonds, you could search for PDB files that have exactly one SSBOND record:</p>

<pre><code><span class="math-container">$ cd $</span>PDB_DIR/structures/divided/pdb/
<span class="math-container">$ zgrep -c ^SSBOND aa/pdb*.ent.gz | grep :1$</span>
aa/pdb2aaq.ent.gz:1
aa/pdb3aad.ent.gz:1
aa/pdb5aap.ent.gz:1
aa/pdb6aa4.ent.gz:1
aa/pdb6aa5.ent.gz:1
</code></pre>

<p>All PDB files (gzipped) take about 30GB of disk space.</p>

<p>The caveat is that some entries are available only in the mmCIF format. Using mmCIF would be slighty more complex: you would need to count <code>_struct_conn.conn_type_id</code> being <code>disulf</code>. And you would need to download 10GB more.</p>

CC BY-SA 4.0
2019-04-18T09:56:06.620Z
Thanks! I need just a few examples, to the 1st method is perfect!
Jake B.
CC BY-SA 4.0
2019-04-18T09:36:38.087Z
2019-04-18T09:36:38.087Z
marcin
<p>I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on <a href="https://www.rcsb.org/" rel="nofollow noreferrer">https://www.rcsb.org/</a>, but no such option, at least I could not find it.</p>

<public-databases><protein-structure>
Proteins with one SS bond?
# Proteins with one SS bond?

(Asked by: username_0 on 2019-04-18)

I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on <https://www.rcsb.org/>, but no such option, at least I could not find it.

**Tags:** public-databases, protein-structure

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## 1 answers

### Answer by username_1 on 2019-04-18. Score: 3 | Accepted answer

In cases when you cannot find answer through the web interface, you can download all the data and search it locally.
Relying on the PDB annotations of SS bonds, you could search for PDB files that have exactly one SSBOND record:
$ cd $PDB_DIR/structures/divided/pdb/
$ zgrep -c ^SSBOND aa/pdb*.ent.gz | grep :1$
aa/pdb2aaq.ent.gz:1
aa/pdb3aad.ent.gz:1
aa/pdb5aap.ent.gz:1
aa/pdb6aa4.ent.gz:1
aa/pdb6aa5.ent.gz:1

All PDB files (gzipped) take about 30GB of disk space.
The caveat is that some entries are available only in the mmCIF format. Using mmCIF would be slighty more complex: you would need to count _struct_conn.conn_type_id being disulf. And you would need to download 10GB more.

> **Comments:**
> **username_0**: Thanks! I need just a few examples, to the 1st method is perfect!  

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