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I wonder how, for purposes of just illustrating some concepts like substrate alignment in the catalytic triad active site, I can quickly and efficiently find a protease structure (irrelevant of what organism exactly) that has a peptide like inhibitor on the PDB database.

Hints appreciated.

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  • $\begingroup$ I'm not a Google search expert but "pdb structure protease peptide inhibitor -non-peptide" seems to provide some useful hits $\endgroup$ – Alan Boyd Jun 21 '14 at 15:44
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Here's one: http://www.rcsb.org/pdb/explore/explore.do?structureId=2IPH. It was crystallized with the inhibitor bound to the protein.

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  • $\begingroup$ How did you find it? $\endgroup$ – TMOTTM Jun 22 '14 at 19:00
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    $\begingroup$ I searched within the pdb for protease inhibitor. Since the inhibitors themselves are not proteins, most of the search results are proteases with inhibitors. $\endgroup$ – prooffreader Jun 22 '14 at 23:48
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go to http://www.uniprot.org and enter the protease accession number you are interested in and look at the 3D structure databases section to see if its PDB file is deciphered or not. I came across this database (http://www.cf.ac.uk/biosi/staffinfo/ehrmann/tools/proteases/allproteases.html) just by typing into google "protease PDB databases"

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