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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.

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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.

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  • $\begingroup$ Thanks! I need just a few examples, to the 1st method is perfect! $\endgroup$ – Jake B. Apr 18 '19 at 9:56

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