4tvg - Revision history

OCA at 07:23, 27 September 2023

2023-09-27T07:23:34Z

←Older revision		Revision as of 07:23, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TVG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene>, <scene name='pdbligand=STA:STATINE'>STA</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]] 2.18Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [https://pdbe.org/4tvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [https://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg 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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [https://pdbe.org/4tvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [https://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:57, 15 March 2023

2023-03-15T10:57:25Z

←Older revision		Revision as of 10:57, 15 March 2023
Line 3:		Line 3:
	<StructureSection load='4tvg' size='340' side='right'caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='4tvg' size='340' side='right'caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tvg]] is a 3 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=4TVG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4TVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TVG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97~~</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA~~</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene>~~</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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [https://pdbe.org/4tvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [https://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [~~http~~://pdbe.org/4tvg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q90EA1_9HIV1 Q90EA1_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Finn, M G~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Kislukhin, A~~]]	+	[[Category: Finn MG]]
-	[[Category: ~~Stout, C D~~]]	+	[[Category: Kislukhin A]]
-	[[Category: ~~Tiefenbrunn, T~~]]	+	[[Category: Stout CD]]
-	[[Category: ~~Allostery]]~~	+	[[Category: Tiefenbrunn T]]
-	~~[[Category: Apo protease]]~~	+
-	~~[[Category: Fragment binding]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 10:20, 25 December 2019

2019-12-25T10:20:42Z

←Older revision		Revision as of 10:20, 25 December 2019
Line 3:		Line 3:
	<StructureSection load='4tvg' size='340' side='right'caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='4tvg' size='340' side='right'caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tvg]] is a 3 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=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://pdbe.org/4tvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg 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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://pdbe.org/4tvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:06, 10 July 2019

2019-07-10T07:06:25Z

←Older revision		Revision as of 07:06, 10 July 2019
Line 1:		Line 1:

	==HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap==		==HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap==
-	<StructureSection load='4tvg' size='340' side='right' caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='4tvg' size='340' side='right'caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Immunodeficiency virus protease\|Immunodeficiency virus protease]]	+	*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Finn, M G]]		[[Category: Finn, M G]]
	[[Category: Kislukhin, A]]		[[Category: Kislukhin, A]]

OCA at 05:51, 6 October 2017

2017-10-06T05:51:14Z

←Older revision		Revision as of 05:51, 6 October 2017
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4tvg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4tvg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Immunodeficiency virus protease\|Immunodeficiency virus protease]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 32:
	[[Category: Apo protease]]		[[Category: Apo protease]]
	[[Category: Fragment binding]]		[[Category: Fragment binding]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 14:32, 11 August 2016

2016-08-11T14:32:13Z

←Older revision		Revision as of 14:32, 11 August 2016
Line 1:		Line 1:
		+
	==HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap==		==HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap==
	<StructureSection load='4tvg' size='340' side='right' caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='4tvg' size='340' side='right' caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum]</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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://pdbe.org/4tvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4tvg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:07, 20 January 2015

2015-01-20T08:07:27Z

←Older revision		Revision as of 08:07, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum]</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=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Finn, M G.]]	+	[[Category: Finn, M G]]
-	[[Category: Kislukhin, A.]]	+	[[Category: Kislukhin, A]]
-	[[Category: Stout, C D.]]	+	[[Category: Stout, C D]]
-	[[Category: Tiefenbrunn, T.]]	+	[[Category: Tiefenbrunn, T]]
	[[Category: Allostery]]		[[Category: Allostery]]
	[[Category: Apo protease]]		[[Category: Apo protease]]
	[[Category: Fragment binding]]		[[Category: Fragment binding]]

OCA at 10:35, 24 September 2014

2014-09-24T10:35:19Z

←Older revision		Revision as of 10:35, 24 September 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap==
		+	<StructureSection load='4tvg' size='340' side='right' caption='[[4tvg]], [[Resolution\|resolution]] 2.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4tvg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K97:3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC+ACID'>K97</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tvh\|4tvh]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tvg RCSB], [http://www.ebi.ac.uk/pdbsum/4tvg PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Molecular docking is a powerful tool used in drug discovery and structural biology for predicting the structures of ligand-receptor complexes. However, the accuracy of docking calculations can be limited by factors such as the neglect of protein reorganization in the scoring function; as a result, ligand screening can produce a high rate of false positive hits. Although absolute binding free energy methods still have difficulty in accurately rank-ordering binders, we believe that they can be fruitfully employed to distinguish binders from nonbinders and reduce the false positive rate. Here we study a set of ligands that dock favorably to a newly discovered, potentially allosteric site on the flap of HIV-1 protease. Fragment binding to this site stabilizes a closed form of protease, which could be exploited for the design of allosteric inhibitors. Twenty-three top-ranked protein-ligand complexes from AutoDock were subject to the free energy screening using two methods, the recently developed binding energy analysis method (BEDAM) and the standard double decoupling method (DDM). Free energy calculations correctly identified most of the false positives (>/=83%) and recovered all the confirmed binders. The results show a gap averaging >/=3.7 kcal/mol, separating the binders and the false positives. We present a formula that decomposes the binding free energy into contributions from the receptor conformational macrostates, which provides insights into the roles of different binding modes. Our binding free energy component analysis further suggests that improving the treatment for the desolvation penalty associated with the unfulfilled polar groups could reduce the rate of false positive hits in docking. The current study demonstrates that the combination of docking with free energy methods can be very useful for more accurate ligand screening against valuable drug targets.

-	~~The entry 4tvg is ON HOLD until Paper Publication~~	+	Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease.,Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM J Phys Chem B. 2014 Sep 17. PMID:25189630<ref>PMID:25189630</ref>

-	~~Authors: Tiefenbrunn~~, T.~~, Kislukhin, A~~., Finn, M.G., Stout, C.D.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Finn, M G.]]
		+	[[Category: Kislukhin, A.]]
		+	[[Category: Stout, C D.]]
		+	[[Category: Tiefenbrunn, T.]]
		+	[[Category: Allostery]]
		+	[[Category: Apo protease]]
		+	[[Category: Fragment binding]]

OCA at 06:58, 9 July 2014

2014-07-09T06:58:40Z

←Older revision		Revision as of 06:58, 9 July 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4tvg is ON HOLD	+	The entry 4tvg is ON HOLD until Paper Publication

	Authors: Tiefenbrunn, T., Kislukhin, A., Finn, M.G., Stout, C.D.		Authors: Tiefenbrunn, T., Kislukhin, A., Finn, M.G., Stout, C.D.

	Description: HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap		Description: HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap

OCA: Protected "4tvg" [edit=sysop:move=sysop]

2014-07-02T07:35:55Z

Protected "4tvg" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:35, 2 July 2014