5yq8 - Revision history

OCA at 08:35, 22 November 2023

OCA — Wed, 22 Nov 2023 08:35:19 GMT

←Older revision		Revision as of 08:35, 22 November 2023
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	<StructureSection load='5yq8' size='340' side='right'caption='[[5yq8]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='5yq8' size='340' side='right'caption='[[5yq8]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yq8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YQ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yq8]] is a 4 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=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YQ8 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=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [~~http~~://pdbe.org/5yq8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 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]] 2.25Å</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=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [https://pdbe.org/5yq8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [https://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kumar, S~~]]	+	[[Category: Leishmania major]]
-	[[Category: ~~Suguna, K~~]]	+	[[Category: Kumar S]]
-	[[Category: ~~Aspartic protease]]~~	+	[[Category: Suguna K]]
-	~~[[Category: Cytoplasmic]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Retropepsin~~]]	+

OCA at 09:25, 21 October 2020

OCA — Wed, 21 Oct 2020 09:25:46 GMT

←Older revision		Revision as of 09:25, 21 October 2020
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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='5yq8' size='340' side='right' caption='[[5yq8]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='5yq8' size='340' side='right'caption='[[5yq8]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yq8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YQ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yq8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YQ8 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [http://pdbe.org/5yq8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 ProSAT]</span></td></tr>	+	</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=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [http://pdbe.org/5yq8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kumar, S]]		[[Category: Kumar, S]]
	[[Category: Suguna, K]]		[[Category: Suguna, K]]

OCA at 19:39, 19 September 2018

OCA — Wed, 19 Sep 2018 19:39:09 GMT

←Older revision		Revision as of 19:39, 19 September 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yq8 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major==
		+	<StructureSection load='5yq8' size='340' side='right' caption='[[5yq8]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yq8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YQ8 FirstGlance]. <br>
		+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [http://pdbe.org/5yq8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 ProSAT]</span></td></tr>
		+	</table>
		+	<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.

-	~~Authors: Suguna, K~~., Kumar, S.	+	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>

-	~~Description: Crystal structure~~ of ~~retroviral protease-like domain~~ of ~~Ddi1 from Leishmania major~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5yq8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kumar, S]]		[[Category: Kumar, S]]
	[[Category: Suguna, K]]		[[Category: Suguna, K]]
		+	[[Category: Aspartic protease]]
		+	[[Category: Cytoplasmic]]
		+	[[Category: Hydrolase]]
		+	[[Category: Retropepsin]]

OCA at 12:14, 11 April 2018

OCA — Wed, 11 Apr 2018 12:14:12 GMT

←Older revision		Revision as of 12:14, 11 April 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yq8 is ON HOLD	+	The entry 5yq8 is ON HOLD until Paper Publication

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

OCA at 04:56, 14 March 2018

OCA — Wed, 14 Mar 2018 04:56:43 GMT

←Older revision		Revision as of 04:56, 14 March 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yq8 is ON HOLD ~~until Paper Publication~~	+	The entry 5yq8 is ON HOLD

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

OCA at 05:56, 6 December 2017

OCA — Wed, 06 Dec 2017 05:56:23 GMT

←Older revision		Revision as of 05:56, 6 December 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yq8 is ON HOLD	+	The entry 5yq8 is ON HOLD until Paper Publication

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

OCA: Protected "5yq8" [edit=sysop:move=sysop]

OCA — Wed, 15 Nov 2017 06:15:39 GMT

Protected "5yq8" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:15, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yq8 is ON HOLD Authors: Suguna, K., Kumar, S. Description: Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major [[Ca...

OCA — Wed, 15 Nov 2017 06:15:38 GMT

New page: '''Unreleased structure''' The entry 5yq8 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 5yq8 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]]