6dgx - Revision history

OCA at 06:05, 11 October 2023

OCA — Wed, 11 Oct 2023 06:05:59 GMT

←Older revision		Revision as of 06:05, 11 October 2023
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	<StructureSection load='6dgx' size='340' side='right'caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6dgx' size='340' side='right'caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DGX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DGX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=017:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE'>017</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</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]] 2.001Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=017:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE'>017</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6dgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgx OCA], [~~http~~://pdbe.org/6dgx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dgx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dgx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgx ProSAT]</span></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=6dgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgx OCA], [https://pdbe.org/6dgx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dgx RCSB], [https://www.ebi.ac.uk/pdbsum/6dgx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72498_9HIV1 Q72498_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lockbaum~~, G J~~]]	+	[[Category: Lockbaum GJ]]
-	[[Category: Schiffer~~, C A]]~~	+	[[Category: Schiffer CA]]
-	~~[[Category: Drug resistance]]~~	+
-	~~[[Category: Hiv]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase inhibitor complex]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Nl4-3]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Protease inhibitor~~]]	+

OCA at 10:08, 18 December 2019

OCA — Wed, 18 Dec 2019 10:08:25 GMT

←Older revision		Revision as of 10:08, 18 December 2019
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	==Crystal structure of HIV-1 Protease NL4-3 WT in complex with darunavir==		==Crystal structure of HIV-1 Protease NL4-3 WT in complex with darunavir==
-	<StructureSection load='6dgx' size='340' side='right' caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='6dgx' size='340' side='right'caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGX FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGX FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lockbaum, G J]]		[[Category: Lockbaum, G J]]
	[[Category: Schiffer, C A]]		[[Category: Schiffer, C A]]

OCA at 08:35, 21 February 2019

OCA — Thu, 21 Feb 2019 08:35:57 GMT

←Older revision		Revision as of 08:35, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6dgx' size='340' side='right' caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6dgx' size='340' side='right' caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=017:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE'>017</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=017:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE'>017</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=6dgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgx OCA], [http://pdbe.org/6dgx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dgx RCSB], [http://www.ebi.ac.uk/pdbsum/6dgx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgx ProSAT]</span></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=6dgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgx OCA], [http://pdbe.org/6dgx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dgx RCSB], [http://www.ebi.ac.uk/pdbsum/6dgx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgx ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:15, 26 December 2018

OCA — Wed, 26 Dec 2018 08:15:25 GMT

←Older revision		Revision as of 08:15, 26 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dgx is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of HIV-1 Protease NL4-3 WT in complex with darunavir==
		+	<StructureSection load='6dgx' size='340' side='right' caption='[[6dgx]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dgx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=017:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE'>017</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6dgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgx OCA], [http://pdbe.org/6dgx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dgx RCSB], [http://www.ebi.ac.uk/pdbsum/6dgx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgx ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82 and I84 that line the S1/S1' pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogs to primary S1' mutations. The analogs had modifications at the hydrophobic P1' moiety compared to DRV to better occupy the unexploited space in the S1' pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analog with the largest P1' moiety, indicating interdependency between the S1' subsite and the flap region. Collective analysis of protease-inhibitor interactions in the crystal structures using principle component analysis was able to distinguish inhibitor identity and relative potency solely based on vdW contacts. Our results reveal the complexity of the interplay between inhibitor P1' moiety and S1' mutations, and validate principle component analyses as a useful tool for distinguishing resistance and inhibitor potency.

-	~~Authors~~:	+	Structural Adaptation of Darunavir Analogs Against Primary Mutations in HIV-1 Protease.,Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Kurt Yilmaz N, Schiffer CA ACS Infect Dis. 2018 Dec 13. doi: 10.1021/acsinfecdis.8b00336. PMID:30543749<ref>PMID:30543749</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6dgx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lockbaum, G J]]
		+	[[Category: Schiffer, C A]]
		+	[[Category: Drug resistance]]
		+	[[Category: Hiv]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase inhibitor complex]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Nl4-3]]
		+	[[Category: Protease]]
		+	[[Category: Protease inhibitor]]

OCA at 05:36, 14 June 2018

OCA — Thu, 14 Jun 2018 05:36:03 GMT

←Older revision		Revision as of 05:36, 14 June 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dgx is ON HOLD	+	The entry 6dgx is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6dgx" [edit=sysop:move=sysop]

OCA — Wed, 30 May 2018 04:06:11 GMT

Protected "6dgx" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:06, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dgx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 May 2018 04:06:10 GMT

New page: '''Unreleased structure''' The entry 6dgx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6dgx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]