1lgw - Revision history

OCA at 09:14, 16 August 2023

OCA — Wed, 16 Aug 2023 09:14:05 GMT

←Older revision		Revision as of 09:14, 16 August 2023
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	<StructureSection load='1lgw' size='340' side='right'caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1lgw' size='340' side='right'caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LGW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=1AN:2~~-~~FLUOROANILINE'>1AN</scene>~~, ~~<scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.85Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]~~ </~~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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [https://pdbe.org/1lgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [https://www.ebi.ac.uk/pdbsum/1lgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgw 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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [https://pdbe.org/1lgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [https://www.ebi.ac.uk/pdbsum/1lgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~LYS_BPT4 LYS_BPT4~~]~~] Helps~~ to ~~release~~ the mature ~~phage~~ particles ~~from~~ the cell ~~wall by breaking~~ down the peptidoglycan.	+	[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Baase WA]]
-	[[Category: Baase~~, W A~~]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W~~]]	+	[[Category: Shoichet BK]]
-	[[Category: Shoichet~~, B K~~]]	+	[[Category: Weaver LH]]
-	[[Category: Weaver~~, L H~~]]	+	[[Category: Wei BQ]]
-	[[Category: Wei~~, B Q]]~~	+
-	~~[[Category: Bacteriolytic enzyme]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 05:54, 28 April 2021

OCA — Wed, 28 Apr 2021 05:54:11 GMT

←Older revision		Revision as of 05:54, 28 April 2021
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	<StructureSection load='1lgw' size='340' side='right'caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1lgw' size='340' side='right'caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LGW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [~~http~~://pdbe.org/1lgw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lgw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgw 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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [https://pdbe.org/1lgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [https://www.ebi.ac.uk/pdbsum/1lgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.	+	[[https://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:10, 24 July 2019

OCA — Wed, 24 Jul 2019 09:10:43 GMT

←Older revision		Revision as of 09:10, 24 July 2019
Line 1:		Line 1:

	==T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline==		==T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline==
-	<StructureSection load='1lgw' size='340' side='right' caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='1lgw' size='340' side='right'caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/1lgw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/1lgw_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 10:50, 18 October 2017

OCA — Wed, 18 Oct 2017 10:50:42 GMT

←Older revision		Revision as of 10:50, 18 October 2017
Line 1:		Line 1:
		+
	==T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline==		==T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline==
	<StructureSection load='1lgw' size='340' side='right' caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1lgw' size='340' side='right' caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://pdbe.org/1lgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw 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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://pdbe.org/1lgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lgw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:29, 11 September 2015

OCA — Fri, 11 Sep 2015 14:29:10 GMT

←Older revision		Revision as of 14:29, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1lgw' size='340' side='right' caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1lgw' size='340' side='right' caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw 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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://pdbe.org/1lgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1lgw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 17:43, 25 December 2014

OCA — Thu, 25 Dec 2014 17:43:47 GMT

←Older revision		Revision as of 17:43, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw 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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Baase, W A.]]	+	[[Category: Baase, W A]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
-	[[Category: Weaver, L H.]]	+	[[Category: Weaver, L H]]
-	[[Category: Wei, B Q.]]	+	[[Category: Wei, B Q]]
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 16:00, 28 September 2014

OCA — Sun, 28 Sep 2014 16:00:49 GMT

←Older revision		Revision as of 16:00, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lgw.~~png~~\|~~left~~\|200px]]	+	==T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline==
		+	<StructureSection load='1lgw' size='340' side='right' caption='[[1lgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AN:2-FLUOROANILINE'>1AN</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[1lgx\|1lgx]], [[1li2\|1li2]], [[1li3\|1li3]], [[1li6\|1li6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lgw RCSB], [http://www.ebi.ac.uk/pdbsum/1lgw PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/1lgw_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Prediction of interaction energies between ligands and their receptors remains a major challenge for structure-based inhibitor discovery. Much effort has been devoted to developing scoring schemes that can successfully rank the affinities of a diverse set of possible ligands to a binding site for which the structure is known. To test these scoring functions, well-characterized experimental systems can be very useful. Here, mutation-created binding sites in T4 lysozyme were used to investigate how the quality of atomic charges and solvation energies affects molecular docking. Atomic charges and solvation energies were calculated for 172,118 molecules in the Available Chemicals Directory using a semi-empirical quantum mechanical approach by the program AMSOL. The database was first screened against the apolar cavity site created by the mutation Leu99Ala (L99A). Compared to the electronegativity-based charges that are widely used, the new charges and desolvation energies improved ranking of known apolar ligands, and better distinguished them from more polar isosteres that are not observed to bind. To investigate whether the new charges had predictive value, the non-polar residue Met102, which forms part of the binding site, was changed to the polar residue glutamine. The structure of the resulting Leu99Ala and Met102Gln double mutant of T4 lysozyme (L99A/M102Q) was determined and the docking calculation was repeated for the new site. Seven representative polar molecules that preferentially docked to the polar versus the apolar binding site were tested experimentally. All seven bind to the polar cavity (L99A/M102Q) but do not detectably bind to the apolar cavity (L99A). Five ligand-bound structures of L99A/M102Q were determined by X-ray crystallography. Docking predictions corresponded to the crystallographic results to within 0.4A RMSD. Improved treatment of partial atomic charges and desolvation energies in database docking appears feasible and leads to better distinction of true ligands. Simple model binding sites, such as L99A and its more polar variants, may find broad use in the development and testing of docking algorithms.

-	~~{{STRUCTURE_1lgw\| PDB=1lgw \| SCENE= }}~~	+	A model binding site for testing scoring functions in molecular docking.,Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK J Mol Biol. 2002 Sep 13;322(2):339-55. PMID:12217695<ref>PMID:12217695</ref>

-	~~===T4 Lysozyme Mutant L99A~~/~~M102Q Bound by 2-fluoroaniline===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12217695}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1lgw]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012217695<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 19:35, 20 October 2012

OCA — Sat, 20 Oct 2012 19:35:31 GMT

←Older revision		Revision as of 19:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1lgw]] is a 1 chain structure ~~of [[Hen Egg-White (HEW) Lysozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA].	+	[[1lgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA].

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

OCA: Protected "1lgw" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 07:51:18 GMT

Protected "1lgw" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:51, 27 July 2012

OCA at 07:51, 27 July 2012

OCA — Fri, 27 Jul 2012 07:51:17 GMT

←Older revision		Revision as of 07:51, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lgw.png\|left\|200px]]		[[Image:1lgw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lgw", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1lgw\| PDB=1lgw \| SCENE= }}		{{STRUCTURE_1lgw\| PDB=1lgw \| SCENE= }}

	===T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline===		===T4 Lysozyme Mutant L99A/M102Q Bound by 2-fluoroaniline===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12217695}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12217695 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12217695}}		{{ABSTRACT_PUBMED_12217695}}

	==About this Structure==		==About this Structure==
-	~~1LGW~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA].	+	[[1lgw]] is a 1 chain structure of [[Hen Egg-White (HEW) Lysozyme]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGW OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12217695~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012217695</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 33:		Line 24:
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 00:33:49 2009''~~	+