5xc1 - Revision history

OCA at 07:59, 22 November 2023

OCA — Wed, 22 Nov 2023 07:59:09 GMT

←Older revision		Revision as of 07:59, 22 November 2023
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	<StructureSection load='5xc1' size='340' side='right'caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='5xc1' size='340' side='right'caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp.~~_ng~~-27 Bacillus sp. ng-27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._NG-27 Bacillus sp. NG-27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S~~-1,2~~-PROPANEDIOL'>PGO</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]] 2.26Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[5xc0\|5xc0]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Endo~~-1,4-~~beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=5xc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xc1 OCA], [https://pdbe.org/5xc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xc1 RCSB], [https://www.ebi.ac.uk/pdbsum/5xc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xc1 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=5xc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xc1 OCA], [https://pdbe.org/5xc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xc1 RCSB], [https://www.ebi.ac.uk/pdbsum/5xc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xc1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O30700_9BACI O30700_9BACI]
	<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: Bacillus sp. ng-27]]	+	[[Category: Bacillus sp. NG-27]]
-	~~[[Category: Endo-1,4-beta-xylanase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bansia, H]]	+	[[Category: Bansia H]]
-	[[Category: Mahanta, P]]	+	[[Category: Mahanta P]]
-	[[Category: Ramakumar, S]]	+	[[Category: Ramakumar S]]
-	~~[[Category: Gh10 xylanase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 06:46, 24 March 2021

OCA — Wed, 24 Mar 2021 06:46:21 GMT

←Older revision		Revision as of 06:46, 24 March 2021
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	<StructureSection load='5xc1' size='340' side='right'caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='5xc1' size='340' side='right'caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_sp._ng-27 Bacillus sp. ng-27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._ng-27 Bacillus sp. ng-27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xc0\|5xc0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5xc0\|5xc0]]</div></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'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://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=5xc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xc1 OCA], [~~http~~://pdbe.org/5xc1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xc1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xc1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xc1 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=5xc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xc1 OCA], [https://pdbe.org/5xc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xc1 RCSB], [https://www.ebi.ac.uk/pdbsum/5xc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xc1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cryptic pockets are visible in ligand-bound protein structures but are occluded in unbound structures. Utilizing these pockets in fragment-based drug-design provides an attractive option for proteins not tractable by classical binding sites. However, owing to their hidden nature, they are difficult to identify. Here, we show that small glycols find cryptic pockets on a diverse set of proteins. Initial crystallography experiments serendipitously revealed the ability of ethylene glycol, a small glycol, to identify a cryptic pocket on the W6A mutant of the RBSX protein (RBSX-W6A). Explicit-solvent molecular dynamics (MD) simulations of RBSX-W6A with the exposed state of the cryptic pocket (ethylene glycol removed) revealed closure of the pocket reiterating that the exposed state of cryptic pockets in general are unstable in the absence of ligands. Also, no change in the pocket was observed for simulations of RBSX-W6A with the occluded state of the cryptic pocket, suggesting that water molecules are not able to open the cryptic pocket. "Cryptic-pocket finding" potential of small glycols was then supported and generalized through additional crystallography experiments, explicit-cosolvent MD simulations, and protein data set construction and analysis. The cryptic pocket on RBSX-W6A was found again upon repeating the crystallography experiments with another small glycol, propylene glycol. Use of ethylene glycol as a probe molecule in cosolvent MD simulations led to the enhanced sampling of the exposed state of experimentally observed cryptic sites on a test set of two proteins (Niemann-Pick C2, Interleukin-2). Further, analyses of protein structures with validated cryptic sites showed that ethylene glycol molecules bind to sites on proteins (Bcl-xL, G-actin, myosin II, and glutamate receptor 2), which become apparent upon binding of biologically relevant ligands. Our study thus suggests potential application of the small glycols in experimental and computational fragment-based approaches to identify cryptic pockets in apparently undruggable and/or difficult targets, making these proteins amenable to drug-design strategies.
		+
		+	Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches.,Bansia H, Mahanta P, Yennawar NH, Ramakumar S J Chem Inf Model. 2021 Mar 22;61(3):1322-1333. doi: 10.1021/acs.jcim.0c01126., Epub 2021 Feb 11. PMID:33570386<ref>PMID:33570386</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xc1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:48, 28 August 2019

OCA — Wed, 28 Aug 2019 15:48:49 GMT

←Older revision		Revision as of 15:48, 28 August 2019
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	==Crystal structure of the complex of an aromatic mutant (W6A) of an alkali thermostable GH10 Xylanase from Bacillus sp. NG-27 with S-1,2-Propanediol==		==Crystal structure of the complex of an aromatic mutant (W6A) of an alkali thermostable GH10 Xylanase from Bacillus sp. NG-27 with S-1,2-Propanediol==
-	<StructureSection load='5xc1' size='340' side='right' caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>	+	<StructureSection load='5xc1' size='340' side='right'caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._ng-27 Bacillus sp. ng-27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xc0\|5xc0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xc0\|5xc0]]</td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus sp. ng-27]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Bansia, H]]		[[Category: Bansia, H]]
	[[Category: Mahanta, P]]		[[Category: Mahanta, P]]

OCA at 06:33, 28 March 2018

OCA — Wed, 28 Mar 2018 06:33:18 GMT

←Older revision		Revision as of 06:33, 28 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xc1 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the complex of an aromatic mutant (W6A) of an alkali thermostable GH10 Xylanase from Bacillus sp. NG-27 with S-1,2-Propanediol==
-		+	<StructureSection load='5xc1' size='340' side='right' caption='[[5xc1]], [[Resolution\|resolution]] 2.26Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xc1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XC1 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xc0\|5xc0]]</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=5xc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xc1 OCA], [http://pdbe.org/5xc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xc1 RCSB], [http://www.ebi.ac.uk/pdbsum/5xc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xc1 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Bansia, H]]
		+	[[Category: Mahanta, P]]
		+	[[Category: Ramakumar, S]]
		+	[[Category: Gh10 xylanase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tim barrel]]

OCA at 12:01, 19 April 2017

OCA — Wed, 19 Apr 2017 12:01:22 GMT

←Older revision		Revision as of 12:01, 19 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xc1 is ON HOLD	+	The entry 5xc1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5xc1" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 12:28:23 GMT

Protected "5xc1" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:28, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xc1 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 12:28:22 GMT

New page: '''Unreleased structure''' The entry 5xc1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xc1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]