5mng - Revision history

OCA at 17:41, 8 November 2023

OCA — Wed, 08 Nov 2023 17:41:12 GMT

←Older revision		Revision as of 17:41, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MNG FirstGlance]. <br>		<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MNG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 0.86Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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'>[https://proteopedia.org/fgij/fg.htm?mol=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [https://pdbe.org/5mng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [https://www.ebi.ac.uk/pdbsum/5mng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng 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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [https://pdbe.org/5mng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [https://www.ebi.ac.uk/pdbsum/5mng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Trypsin]]~~	+	[[Category: Heine A]]
-	[[Category: Heine, A]]	+	[[Category: Klebe G]]
-	[[Category: Klebe, G]]	+	[[Category: Schiebel J]]
-	[[Category: Schiebel, J]]	+
-	~~[[Category: Hydrogen bonding]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein-ligand interaction]]~~	+
-	~~[[Category: Protonation~~]]	+

OCA at 10:25, 4 August 2021

OCA — Wed, 04 Aug 2021 10:25:38 GMT

←Older revision		Revision as of 10:25, 4 August 2021
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	<StructureSection load='5mng' size='340' side='right'caption='[[5mng]], [[Resolution\|resolution]] 0.86Å' scene=''>		<StructureSection load='5mng' size='340' side='right'caption='[[5mng]], [[Resolution\|resolution]] 0.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MNG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MNG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=~~BAM~~:BENZAMIDINE'>~~BAM~~</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [~~http~~://pdbe.org/5mng PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mng PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng 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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [https://pdbe.org/5mng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [https://www.ebi.ac.uk/pdbsum/5mng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:23, 19 August 2020

OCA — Wed, 19 Aug 2020 07:23:58 GMT

←Older revision		Revision as of 07:23, 19 August 2020
Line 1:		Line 1:

	==Cationic trypsin in complex with benzamidine (deuterated sample at 100 K)==		==Cationic trypsin in complex with benzamidine (deuterated sample at 100 K)==
-	<StructureSection load='5mng' size='340' side='right' caption='[[5mng]], [[Resolution\|resolution]] 0.86Å' scene=''>	+	<StructureSection load='5mng' size='340' side='right'caption='[[5mng]], [[Resolution\|resolution]] 0.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MNG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MNG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAM:BENZAMIDINE'>BAM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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" id="ligandDat"><scene name='pdbligand=BAM:BENZAMIDINE'>BAM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [http://pdbe.org/5mng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [http://www.ebi.ac.uk/pdbsum/5mng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng ProSAT]</span></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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [http://pdbe.org/5mng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [http://www.ebi.ac.uk/pdbsum/5mng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5mng" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mng" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Trypsin 3D structures\|Trypsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
		+	[[Category: Large Structures]]
	[[Category: Trypsin]]		[[Category: Trypsin]]
	[[Category: Heine, A]]		[[Category: Heine, A]]

OCA at 07:44, 12 September 2018

OCA — Wed, 12 Sep 2018 07:44:37 GMT

←Older revision		Revision as of 07:44, 12 September 2018
Line 8:		Line 8:
	<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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [http://pdbe.org/5mng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [http://www.ebi.ac.uk/pdbsum/5mng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng 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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [http://pdbe.org/5mng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [http://www.ebi.ac.uk/pdbsum/5mng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions </=1.5 A in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.
		+
		+	Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.,Schiebel J, Gaspari R, Wulsdorf T, Ngo K, Sohn C, Schrader TE, Cavalli A, Ostermann A, Heine A, Klebe G Nat Commun. 2018 Sep 3;9(1):3559. doi: 10.1038/s41467-018-05769-2. PMID:30177695<ref>PMID:30177695</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5mng" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:46, 17 January 2018

OCA — Wed, 17 Jan 2018 06:46:10 GMT

←Older revision		Revision as of 06:46, 17 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mng is ~~ON HOLD until Paper Publication~~	+	==Cationic trypsin in complex with benzamidine (deuterated sample at 100 K)==
-		+	<StructureSection load='5mng' size='340' side='right' caption='[[5mng]], [[Resolution\|resolution]] 0.86Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MNG FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAM:BENZAMIDINE'>BAM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=5mng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mng OCA], [http://pdbe.org/5mng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mng RCSB], [http://www.ebi.ac.uk/pdbsum/5mng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mng ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Trypsin]]
		+	[[Category: Heine, A]]
		+	[[Category: Klebe, G]]
		+	[[Category: Schiebel, J]]
		+	[[Category: Hydrogen bonding]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein-ligand interaction]]
		+	[[Category: Protonation]]

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

OCA — Thu, 22 Dec 2016 19:12:54 GMT

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

←Older revision

Revision as of 19:12, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mng is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 22 Dec 2016 19:12:53 GMT

New page: '''Unreleased structure''' The entry 5mng is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5mng is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]