3huk - Revision history

OCA at 07:31, 6 September 2023

OCA — Wed, 06 Sep 2023 07:31:36 GMT

←Older revision		Revision as of 07:31, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3huk' size='340' side='right'caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>		<StructureSection load='3huk' size='340' side='right'caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HUK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BME:BETA~~-~~MERCAPTOETHANOL'>BME</scene>~~, ~~<scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.29Å</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]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">E ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [https://pdbe.org/3huk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [https://www.ebi.ac.uk/pdbsum/3huk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3huk 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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [https://pdbe.org/3huk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [https://www.ebi.ac.uk/pdbsum/3huk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3huk 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]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Boyce SE]]
-	[[Category: Boyce~~, S E~~]]	+	[[Category: Dill KA]]
-	[[Category: Dill~~, K A~~]]	+	[[Category: Graves AP]]
-	[[Category: Graves~~, A P~~]]	+	[[Category: Mobley DL]]
-	[[Category: Mobley~~, D L~~]]	+	[[Category: Rocklin GJ]]
-	[[Category: Rocklin~~, G J~~]]	+	[[Category: Shoichet BK]]
-	[[Category: Shoichet~~, B K]]~~	+
-	~~[[Category: Antimicrobial]]~~	+
-	~~[[Category: Bacteriolytic enzyme]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:04, 13 October 2021

OCA — Wed, 13 Oct 2021 12:04:18 GMT

←Older revision		Revision as of 12:04, 13 October 2021
Line 1:		Line 1:

	==Benzylacetate in complex with T4 lysozyme L99A/M102Q==		==Benzylacetate in complex with T4 lysozyme L99A/M102Q==
-	<StructureSection load='3huk' size='340' side='right' caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>	+	<StructureSection load='3huk' size='340' side='right'caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</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]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [~~http~~://pdbe.org/3huk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3huk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3huk 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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [https://pdbe.org/3huk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [https://www.ebi.ac.uk/pdbsum/3huk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3huk 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]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hu/3huk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hu/3huk_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 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]

OCA at 13:31, 5 August 2016

OCA — Fri, 05 Aug 2016 13:31:33 GMT

←Older revision		Revision as of 13:31, 5 August 2016
Line 1:		Line 1:
		+
	==Benzylacetate in complex with T4 lysozyme L99A/M102Q==		==Benzylacetate in complex with T4 lysozyme L99A/M102Q==
	<StructureSection load='3huk' size='340' side='right' caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>		<StructureSection load='3huk' size='340' side='right' caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HUK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 ~~Enterobacteria phage T4~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [http://www.ebi.ac.uk/pdbsum/3huk 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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [http://pdbe.org/3huk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [http://www.ebi.ac.uk/pdbsum/3huk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3huk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3huk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3huk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]

OCA at 19:13, 25 December 2014

OCA — Thu, 25 Dec 2014 19:13:31 GMT

←Older revision		Revision as of 19:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HUK FirstGlance]. <br>		<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HUK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [http://www.ebi.ac.uk/pdbsum/3huk 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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [http://www.ebi.ac.uk/pdbsum/3huk 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 36:		Line 38:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Boyce, S E.]]	+	[[Category: Boyce, S E]]
-	[[Category: Dill, K A.]]	+	[[Category: Dill, K A]]
-	[[Category: Graves, A P.]]	+	[[Category: Graves, A P]]
-	[[Category: Mobley, D L.]]	+	[[Category: Mobley, D L]]
-	[[Category: Rocklin, G J.]]	+	[[Category: Rocklin, G J]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 11:04, 29 September 2014

OCA — Mon, 29 Sep 2014 11:04:26 GMT

←Older revision		Revision as of 11:04, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3huk.~~png~~\|~~left~~\|200px]]	+	==Benzylacetate in complex with T4 lysozyme L99A/M102Q==
		+	<StructureSection load='3huk' size='340' side='right' caption='[[3huk]], [[Resolution\|resolution]] 1.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3huk]] 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=3HUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HUK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=J0Z:BENZYL+ACETATE'>J0Z</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgu\|1lgu]], [[3ht6\|3ht6]], [[3ht7\|3ht7]], [[3ht8\|3ht8]], [[3ht9\|3ht9]], [[3htb\|3htb]], [[3htd\|3htd]], [[3htf\|3htf]], [[3hug\|3hug]], [[3hu8\|3hu8]], [[3hu9\|3hu9]], [[3hua\|3hua]], [[3huq\|3huq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</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=3huk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3huk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3huk RCSB], [http://www.ebi.ac.uk/pdbsum/3huk 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/hu/3huk_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 ==
		+	We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed "relative" binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 kcal/mol (phenol) and 1.1 kcal/mol (catechol). To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0 A (diverse set), 1.8 A (phenol-derived predictions), and 1.2 A (catechol-derived predictions). We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe that these results can help guide future improvements in physics-based absolute binding free energy methods.

-	~~{{STRUCTURE_3huk\| PDB=3huk \| SCENE= }}~~	+	Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.,Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK J Mol Biol. 2009 Dec 11;394(4):747-63. Epub 2009 Sep 24. PMID:19782087<ref>PMID:19782087</ref>

-	~~===Benzylacetate in complex with T4 lysozyme L99A~~/~~M102Q===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19782087}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3huk]] 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=3HUK 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:019782087<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 20:25, 20 October 2012

OCA — Sat, 20 Oct 2012 20:25:31 GMT

←Older revision		Revision as of 20:25, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3huk]] 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=3HUK OCA].	+	[[3huk]] 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=3HUK OCA].

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

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

OCA — Fri, 27 Jul 2012 10:27:01 GMT

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

←Older revision

Revision as of 10:27, 27 July 2012

OCA at 10:27, 27 July 2012

OCA — Fri, 27 Jul 2012 10:27:00 GMT

←Older revision		Revision as of 10:27, 27 July 2012
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-	{{Seed}}
	[[Image:3huk.png\|left\|200px]]		[[Image:3huk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3huk", 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_3huk\| PDB=3huk \| SCENE= }}		{{STRUCTURE_3huk\| PDB=3huk \| SCENE= }}

	===Benzylacetate in complex with T4 lysozyme L99A/M102Q===		===Benzylacetate in complex with T4 lysozyme L99A/M102Q===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19782087}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19782087 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19782087}}		{{ABSTRACT_PUBMED_19782087}}

	==About this Structure==		==About this Structure==
-	~~3HUK~~ 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=3HUK OCA].	+	[[3huk]] 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=3HUK OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19782087~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019782087</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 36:		Line 27:
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 15:07:49 2010''

OCA at 13:07, 28 January 2010

OCA — Thu, 28 Jan 2010 13:07:49 GMT

←Older revision		Revision as of 13:07, 28 January 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3HUK 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=3HUK OCA].	+	3HUK 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=3HUK OCA].

	==Reference==		==Reference==
Line 37:		Line 37:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Dec 23 09~~:04:~~22 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 15:07:49 2010''

OCA at 07:04, 23 December 2009

OCA — Wed, 23 Dec 2009 07:04:23 GMT

←Older revision		Revision as of 07:04, 23 December 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3huk.~~jpg~~\|left\|200px]]	+	[[Image:3huk.png\|left\|200px]]

	<!--		<!--
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	[[Category: Hydrolase]]		[[Category: Hydrolase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Nov 4 10~~:58:25 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 23 09:04:22 2009''