5mny - Revision history

OCA at 17:41, 8 November 2023

OCA — Wed, 08 Nov 2023 17:41:37 GMT

←Older revision		Revision as of 17:41, 8 November 2023
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	<StructureSection load='5mny' size='340' side='right'caption='[[5mny]], [[Resolution\|resolution]] 1.43Å' scene=''>		<StructureSection load='5mny' size='340' side='right'caption='[[5mny]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mny]] 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=5MNY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mny]] 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=5MNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MNY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=WOT:PHENYLAZANIUM'>WOT</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution\|Resolution]] 1.43Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=WOT:PHENYLAZANIUM'>WOT</scene></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=5mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mny OCA], [~~http~~://pdbe.org/5mny PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mny RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mny PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mny 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=5mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mny OCA], [https://pdbe.org/5mny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mny RCSB], [https://www.ebi.ac.uk/pdbsum/5mny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mny 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 ==
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	[[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: Ostermann A]]
-	[[Category: Ostermann, A]]	+	[[Category: Schiebel J]]
-	[[Category: Schiebel, J]]	+	[[Category: Schrader TE]]
-	[[Category: Schrader~~, T E]]~~	+
-	~~[[Category: Hydrogen bonding]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein-ligand interaction]]~~	+
-	~~[[Category: Protonation~~]]	+

OCA at 07:24, 19 August 2020

OCA — Wed, 19 Aug 2020 07:24:31 GMT

←Older revision		Revision as of 07:24, 19 August 2020
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	==Neutron structure of cationic trypsin in complex with aniline==		==Neutron structure of cationic trypsin in complex with aniline==
-	<StructureSection load='5mny' size='340' side='right' caption='[[5mny]], [[Resolution\|resolution]] 1.43Å' scene=''>	+	<StructureSection load='5mny' size='340' side='right'caption='[[5mny]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mny]] 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=5MNY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mny]] 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=5MNY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MNY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=WOT:PHENYLAZANIUM'>WOT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=WOT:PHENYLAZANIUM'>WOT</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=5mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mny OCA], [http://pdbe.org/5mny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mny RCSB], [http://www.ebi.ac.uk/pdbsum/5mny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mny 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=5mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mny OCA], [http://pdbe.org/5mny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mny RCSB], [http://www.ebi.ac.uk/pdbsum/5mny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mny ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Trypsin\|Trypsin]]	+	*[[Trypsin 3D structures\|Trypsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		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 08:49, 14 November 2018

OCA — Wed, 14 Nov 2018 08:49:54 GMT

←Older revision		Revision as of 08:49, 14 November 2018
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5mny" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mny" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Trypsin\|Trypsin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:41, 24 May 2017

OCA — Wed, 24 May 2017 13:41:43 GMT

←Older revision		Revision as of 13:41, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mny is ~~ON HOLD until Paper~~ Publication	+	==Neutron structure of cationic trypsin in complex with aniline==
		+	<StructureSection load='5mny' size='340' side='right' caption='[[5mny]], [[Resolution\|resolution]] 1.43Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mny]] 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=5MNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MNY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=WOT:PHENYLAZANIUM'>WOT</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='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=5mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mny OCA], [http://pdbe.org/5mny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mny RCSB], [http://www.ebi.ac.uk/pdbsum/5mny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mny ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogen atoms play a key role in protein-ligand recognition. They determine the quality of established H-bonding networks and define the protonation of bound ligands. Structural visualization of H atoms by X-ray crystallography is rarely possible. We used neutron diffraction to determine the positions of the hydrogen atoms in the ligands aniline and 2-aminopyridine bound to the archetypical serine protease trypsin. The resulting structures show the best resolution so far achieved for proteins larger than 100 residues and allow an accurate description of the protonation states and interactions with nearby water molecules. Despite its low pKa of 4.6 and a large distance of 3.6 A to the charged Asp189 at the bottom of the S1 pocket, the amino group of aniline becomes protonated, whereas in 2-aminopyridine, the pyridine nitrogen picks up the proton although its amino group is 1.6 A closer to Asp189. Therefore, apart from charge-charge distances, tautomer stability is decisive for the resulting binding poses, an aspect that is pivotal for predicting correct binding.

-	~~Authors~~:	+	Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin.,Schiebel J, Gaspari R, Sandner A, Ngo K, Gerber HD, Cavalli A, Ostermann A, Heine A, Klebe G Angew Chem Int Ed Engl. 2017 Apr 18;56(17):4887-4890. doi:, 10.1002/anie.201701038. Epub 2017 Mar 28. PMID:28371253<ref>PMID:28371253</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5mny" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Trypsin]]
		+	[[Category: Heine, A]]
		+	[[Category: Klebe, G]]
		+	[[Category: Ostermann, A]]
		+	[[Category: Schiebel, J]]
		+	[[Category: Schrader, T E]]
		+	[[Category: Hydrogen bonding]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein-ligand interaction]]
		+	[[Category: Protonation]]

OCA at 13:46, 2 January 2017

OCA — Mon, 02 Jan 2017 13:46:27 GMT

←Older revision		Revision as of 13:46, 2 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Thu, 22 Dec 2016 19:13:52 GMT

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

←Older revision

Revision as of 19:13, 22 December 2016

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

OCA — Thu, 22 Dec 2016 19:13:51 GMT

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

New page

'''Unreleased structure'''

The entry 5mny is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]