5tzo - Revision history

OCA at 14:24, 6 March 2024

2024-03-06T14:24:21Z

←Older revision		Revision as of 14:24, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5tzo' size='340' side='right'caption='[[5tzo]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='5tzo' size='340' side='right'caption='[[5tzo]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tzo]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TZO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tzo]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TZO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=7V7:N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide'>7V7</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.67Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tvv\|5tvv]]~~, [[~~5tvy~~\|~~5tvy~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7V7:N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide'>7V7</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~xynA, BSU18840 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=224308 BACSU]~~)~~</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=5tzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzo OCA], [https://pdbe.org/5tzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tzo RCSB], [https://www.ebi.ac.uk/pdbsum/5tzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzo ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~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=5tzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzo OCA], [~~http~~://pdbe.org/5tzo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tzo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tzo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzo ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/XYNA_BACSU XYNA_BACSU]
-	We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.	+
-		+
-	Computational design of environmental sensors for the potent opioid fentanyl.,Bick MJ, Greisen PJ, Morey KJ, Antunes MS, La D, Sankaran B, Reymond L, Johnsson K, Medford JI, Baker D Elife. 2017 Sep 19;6. pii: ~~e28909. doi: 10.7554~~/~~eLife.28909. PMID:28925919<ref>PMID:28925919<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5tzo" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu]]~~	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-	~~[[Category: Endo-1,4-beta-xylanase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Antunes~~, M S~~]]	+	[[Category: Antunes MS]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Bick~~, M J~~]]	+	[[Category: Bick MJ]]
-	[[Category: Greisen~~, P J~~]]	+	[[Category: Greisen PJ]]
-	[[Category: Johnsson, K]]	+	[[Category: Johnsson K]]
-	[[Category: La, D]]	+	[[Category: La D]]
-	[[Category: Medford~~, J I~~]]	+	[[Category: Medford JI]]
-	[[Category: Morey~~, K J~~]]	+	[[Category: Morey KJ]]
-	[[Category: Reymond, L]]	+	[[Category: Reymond L]]
-	[[Category: Sankaran, B]]	+	[[Category: Sankaran B]]
-	~~[[Category: Computational design]]~~	+
-	~~[[Category: Fentanyl]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:27, 4 December 2019

2019-12-04T09:27:43Z

←Older revision		Revision as of 09:27, 4 December 2019
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	==Computationally Designed Fentanyl Binder - Fen49*-Complex==		==Computationally Designed Fentanyl Binder - Fen49*-Complex==
-	<StructureSection load='5tzo' size='340' side='right' caption='[[5tzo]], [[Resolution\|resolution]] 1.67Å' scene=''>	+	<StructureSection load='5tzo' size='340' side='right'caption='[[5tzo]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tzo]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tzo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TZO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7V7:N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide'>7V7</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7V7:N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide'>7V7</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tvv\|5tvv]], [[5tvy\|5tvy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tvv\|5tvv]], [[5tvy\|5tvy]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xynA, BSU18840 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=5tzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzo OCA], [http://pdbe.org/5tzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tzo RCSB], [http://www.ebi.ac.uk/pdbsum/5tzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzo 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=5tzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzo OCA], [http://pdbe.org/5tzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tzo RCSB], [http://www.ebi.ac.uk/pdbsum/5tzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzo ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Antunes, M S]]		[[Category: Antunes, M S]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 09:31, 4 October 2017

2017-10-04T09:31:01Z

←Older revision		Revision as of 09:31, 4 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tzo is ~~ON HOLD until Paper~~ Publication	+	==Computationally Designed Fentanyl Binder - Fen49*-Complex==
		+	<StructureSection load='5tzo' size='340' side='right' caption='[[5tzo]], [[Resolution\|resolution]] 1.67Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tzo]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TZO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7V7:N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide'>7V7</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tvv\|5tvv]], [[5tvy\|5tvy]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=5tzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzo OCA], [http://pdbe.org/5tzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tzo RCSB], [http://www.ebi.ac.uk/pdbsum/5tzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzo ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.

-	~~Authors~~:	+	Computational design of environmental sensors for the potent opioid fentanyl.,Bick MJ, Greisen PJ, Morey KJ, Antunes MS, La D, Sankaran B, Reymond L, Johnsson K, Medford JI, Baker D Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909. PMID:28925919<ref>PMID:28925919</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5tzo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Antunes, M S]]
		+	[[Category: Baker, D]]
		+	[[Category: Bick, M J]]
		+	[[Category: Greisen, P J]]
		+	[[Category: Johnsson, K]]
		+	[[Category: La, D]]
		+	[[Category: Medford, J I]]
		+	[[Category: Morey, K J]]
		+	[[Category: Reymond, L]]
		+	[[Category: Sankaran, B]]
		+	[[Category: Computational design]]
		+	[[Category: Fentanyl]]
		+	[[Category: Hydrolase]]

OCA at 16:10, 1 February 2017

2017-02-01T16:10:19Z

←Older revision		Revision as of 16:10, 1 February 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2016-12-09T18:07:11Z

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

←Older revision

Revision as of 18:07, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5tzo is ON HOLD Authors: Description: Category: Unreleased Structures

2016-12-09T18:07:10Z

New page: '''Unreleased structure''' The entry 5tzo is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5tzo is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]