View source for 5ys4


==Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major==
<StructureSection load='5ys4' size='340' side='right'caption='[[5ys4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ys4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YS4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YS4 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ys4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ys4 OCA], [https://pdbe.org/5ys4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ys4 RCSB], [https://www.ebi.ac.uk/pdbsum/5ys4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ys4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DDI1_LEIMA DDI1_LEIMA] Aspartic protease (PubMed:22933181, PubMed:21266539).<ref>PMID:22933181</ref> <ref>PMID:21266539</ref> 
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== Publication Abstract from PubMed ==
DNA damage-inducible 1 (Ddi1) is a multidomain protein with one of the domains being retropepsin-like. HIV-1 protease inhibitors were found to reduce opportunistic infections caused by pathogens like Leishmania and Plasmodium, and some of them were shown to inhibit the growth of these parasites. In Leishmania, Ddi1 was identified as a likely target of the inhibitors. We report the crystal structure of the retropepsin-like domain of Ddi1 from Leishmania major as a dimer with clear density for the critical 'flap' region. We have characterized binding with one of the HIV-1 protease inhibitors in solution using bio-layer interferometry and by docking. Further, we have performed molecular dynamics (MD) simulation studies that show that the protein undergoes a conformational change from open to semi-open and closed forms with the closing of the flexible flap over the active site.

Crystal structure of the retroviral protease-like domain of a protozoal DNA damage-inducible 1 protein.,Kumar S, Suguna K FEBS Open Bio. 2018 Aug 3;8(9):1379-1394. doi: 10.1002/2211-5463.12491., eCollection 2018 Sep. PMID:30186740<ref>PMID:30186740</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Leishmania major]]
[[Category: Kumar S]]
[[Category: Suguna K]]