3uuz - Revision history

OCA at 14:08, 14 March 2024

OCA — Thu, 14 Mar 2024 14:08:55 GMT

←Older revision		Revision as of 14:08, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3uuz' size='340' side='right'caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3uuz' size='340' side='right'caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uuz]] is a 2 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=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.1Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [https://pdbe.org/3uuz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [https://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz 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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [https://pdbe.org/3uuz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [https://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
-	Abstract A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.	+
-		+
-	~~Correlating structure and ligand affinity in drug discovery~~: a cautionary tale involving second shell residues.,Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Brauer U, Ursel C, Steinmetzer P, Sturzebecher J, Schweinitz A, Steinmetzer T, Stubbs MT Biol Chem. 2014 Jul 1;395(7-8):891-903. doi: 10.1515/~~hsz-2014-0158. PMID:25003390<ref>PMID:25003390<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3uuz" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Trypsin 3D structures\|Trypsin 3D structures]]		*[[Trypsin 3D structures\|Trypsin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Trypsin]]~~	+	[[Category: Kolenko P]]
-	[[Category: Kolenko, P]]	+	[[Category: Neumann P]]
-	[[Category: Neumann, P]]	+	[[Category: Stubbs MT]]
-	[[Category: Stubbs~~, M T~~]]	+	[[Category: Tziridis A]]
-	[[Category: Tziridis, A]]	+
-	~~[[Category: Duodenum]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Trypsin-like serine protease~~]]	+

OCA at 08:08, 20 July 2022

OCA — Wed, 20 Jul 2022 08:08:42 GMT

←Older revision		Revision as of 08:08, 20 July 2022
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	<StructureSection load='3uuz' size='340' side='right'caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3uuz' size='340' side='right'caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</div></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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [~~http~~://pdbe.org/3uuz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz 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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [https://pdbe.org/3uuz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [https://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:46, 9 September 2020

OCA — Wed, 09 Sep 2020 10:46:46 GMT

←Older revision		Revision as of 10:46, 9 September 2020
Line 1:		Line 1:

	==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==		==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==
-	<StructureSection load='3uuz' size='340' side='right' caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3uuz' size='340' side='right'caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://pdbe.org/3uuz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz 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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://pdbe.org/3uuz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Trypsin\|Trypsin]]	+	*[[Trypsin 3D structures\|Trypsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Bovin]]		[[Category: Bovin]]
		+	[[Category: Large Structures]]
	[[Category: Trypsin]]		[[Category: Trypsin]]
	[[Category: Kolenko, P]]		[[Category: Kolenko, P]]

OCA at 08:10, 11 August 2016

OCA — Thu, 11 Aug 2016 08:10:41 GMT

←Older revision		Revision as of 08:10, 11 August 2016
Line 1:		Line 1:
		+
	==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==		==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==
	<StructureSection load='3uuz' size='340' side='right' caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3uuz' size='340' side='right' caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz 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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://pdbe.org/3uuz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uuz 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 3uuz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 12:27, 5 January 2015

OCA — Mon, 05 Jan 2015 12:27:56 GMT

←Older revision		Revision as of 12:27, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz 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=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz 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 25:		Line 25:
	[[Category: Bovin]]		[[Category: Bovin]]
	[[Category: Trypsin]]		[[Category: Trypsin]]
-	[[Category: Kolenko, P.]]	+	[[Category: Kolenko, P]]
-	[[Category: Neumann, P.]]	+	[[Category: Neumann, P]]
-	[[Category: Stubbs, M T.]]	+	[[Category: Stubbs, M T]]
-	[[Category: Tziridis, A.]]	+	[[Category: Tziridis, A]]
	[[Category: Duodenum]]		[[Category: Duodenum]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 09:12, 16 July 2014

OCA — Wed, 16 Jul 2014 09:12:15 GMT

←Older revision		Revision as of 09:12, 16 July 2014
Line 1:		Line 1:
-	[[~~Image:~~3uuz.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==
		+	<StructureSection load='3uuz' size='340' side='right' caption='[[3uuz]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3uuz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0CB:{[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL][4-({1-[(1E)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)PHENYL]SULFAMOYL}ACETIC+ACID'>0CB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v2k\|1v2k]], [[3unq\|3unq]], [[3uns\|3uns]], [[3unp\|3unp]], [[3upe\|3upe]], [[3uqo\|3uqo]], [[3uqv\|3uqv]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uuz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uuz RCSB], [http://www.ebi.ac.uk/pdbsum/3uuz PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Abstract A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.

-	~~{{STRUCTURE_3uuz\| PDB=3uuz \| SCENE= }}~~	+	Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.,Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Brauer U, Ursel C, Steinmetzer P, Sturzebecher J, Schweinitz A, Steinmetzer T, Stubbs MT Biol Chem. 2014 Jul 1;395(7-8):891-903. doi: 10.1515/hsz-2014-0158. PMID:25003390<ref>PMID:25003390</ref>

-	~~===Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	==~~About this Structure~~==	+	*[[Trypsin\|Trypsin]]
-	[[~~3uuz~~]] ~~is a 2 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=3UUZ OCA].~~	+	== References ==
-	[[Category: ~~Bos taurus~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bovin]]
	[[Category: Trypsin]]		[[Category: Trypsin]]
	[[Category: Kolenko, P.]]		[[Category: Kolenko, P.]]

OCA at 10:55, 5 December 2012

OCA — Wed, 05 Dec 2012 10:55:38 GMT

←Older revision		Revision as of 10:55, 5 December 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3uuz.jpg\|left\|200px]]

-	~~The entry~~ 3uuz ~~is ON HOLD~~ ~~until Nov 29 2013~~	+	{{STRUCTURE_3uuz\| PDB=3uuz \| SCENE= }}

-	~~Authors: Tziridis, A., Neumann, P., Kolenko, P., Stubbs, M.T.~~	+	===Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor===

-	~~Description: Bovine trypsin variant X(triplePhe227) in complex~~ with ~~small molecule~~ inhibitor	+
		+	==About this Structure==
		+	[[3uuz]] is a 2 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=3UUZ OCA].
		+	[[Category: Bos taurus]]
		+	[[Category: Trypsin]]
		+	[[Category: Kolenko, P.]]
		+	[[Category: Neumann, P.]]
		+	[[Category: Stubbs, M T.]]
		+	[[Category: Tziridis, A.]]
		+	[[Category: Duodenum]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Protein binding]]
		+	[[Category: Trypsin-like serine protease]]

OCA at 06:38, 10 October 2012

OCA — Wed, 10 Oct 2012 06:38:12 GMT

←Older revision		Revision as of 06:38, 10 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3uuz is ON HOLD until ~~Paper Publication~~	+	The entry 3uuz is ON HOLD until Nov 29 2013

	Authors: Tziridis, A., Neumann, P., Kolenko, P., Stubbs, M.T.		Authors: Tziridis, A., Neumann, P., Kolenko, P., Stubbs, M.T.

	Description: Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor		Description: Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor

OCA at 11:12, 14 December 2011

OCA — Wed, 14 Dec 2011 11:12:39 GMT

←Older revision		Revision as of 11:12, 14 December 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3uuz is ON HOLD	+	The entry 3uuz is ON HOLD until Paper Publication

	Authors: Tziridis, A., Neumann, P., Kolenko, P., Stubbs, M.T.		Authors: Tziridis, A., Neumann, P., Kolenko, P., Stubbs, M.T.

	Description: Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor		Description: Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor

OCA: Protected "3uuz" [edit=sysop:move=sysop]

OCA — Wed, 07 Dec 2011 07:39:58 GMT

Protected "3uuz" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:39, 7 December 2011