5ys4 - Revision history

OCA at 08:36, 22 November 2023

OCA — Wed, 22 Nov 2023 08:36:22 GMT

←Older revision		Revision as of 08:36, 22 November 2023
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	==Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major==		==Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major==
-	<StructureSection load='5ys4' size='340' side='right'caption='[[5ys4]]' scene=''>	+	<StructureSection load='5ys4' size='340' side='right'caption='[[5ys4]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>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 [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YS4 FirstGlance]. <br>	+	<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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ys4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ys4 OCA], [~~http~~://pdbe.org/5ys4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ys4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ys4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ys4 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</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>		</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>
		+	<div style="background-color:#fffaf0;">
		+	== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ys4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Leishmania major]]
	[[Category: Kumar S]]		[[Category: Kumar S]]
	[[Category: Suguna K]]		[[Category: Suguna K]]

OCA at 09:26, 21 October 2020

OCA — Wed, 21 Oct 2020 09:26:41 GMT

←Older revision		Revision as of 09:26, 21 October 2020
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-	'''Unreleased structure'''

-	~~The entry 5ys4 is ON HOLD until Paper Publication~~	+	==Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major==
-		+	<StructureSection load='5ys4' size='340' side='right'caption='[[5ys4]]' scene=''>
-	~~Authors: Suguna, K., Kumar, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>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 [http://proteopedia.org/fgij/fg.htm?mol=5YS4 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ys4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ys4 OCA], [http://pdbe.org/5ys4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ys4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ys4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ys4 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kumar, S]]	+	__TOC__
-	[[Category: Suguna, K]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kumar S]]
		+	[[Category: Suguna K]]

OCA at 06:06, 17 October 2018

OCA — Wed, 17 Oct 2018 06:06:40 GMT

←Older revision		Revision as of 06:06, 17 October 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ys4 is ON HOLD	+	The entry 5ys4 is ON HOLD until Paper Publication

	Authors: Suguna, K., Kumar, S.		Authors: Suguna, K., Kumar, S.

OCA: Protected "5ys4" [edit=sysop:move=sysop]

OCA — Wed, 22 Nov 2017 06:26:36 GMT

Protected "5ys4" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:26, 22 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ys4 is ON HOLD Authors: Suguna, K., Kumar, S. Description: Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major [[Ca...

OCA — Wed, 22 Nov 2017 06:26:35 GMT

New page: '''Unreleased structure''' The entry 5ys4 is ON HOLD Authors: Suguna, K., Kumar, S. Description: Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major [[Ca...

New page

'''Unreleased structure'''

The entry 5ys4 is ON HOLD

Authors: Suguna, K., Kumar, S.

Description: Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major
[[Category: Unreleased Structures]]
[[Category: Kumar, S]]
[[Category: Suguna, K]]