2ou0 - Revision history

OCA at 10:48, 30 August 2023

2023-08-30T10:48:37Z

←Older revision		Revision as of 10:48, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2ou0' size='340' side='right'caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2ou0' size='340' side='right'caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MR3:1~~-~~METHYL-1H-PYRROLE'>MR3</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]] 1.94Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[181l\|181l]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MR3:1-METHYL-1H-PYRROLE'>MR3</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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [https://pdbe.org/2ou0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ou0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ou0 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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [https://pdbe.org/2ou0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ou0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ou0 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: Graves AP]]
-	[[Category: Graves~~, A P~~]]	+	[[Category: Shoichet BK]]
-	[[Category: Shoichet~~, B K]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Model system]]~~	+
-	~~[[Category: Protein-ligand complex~~]]	+

OCA at 13:05, 9 June 2021

2021-06-09T13:05:51Z

←Older revision		Revision as of 13:05, 9 June 2021
Line 1:		Line 1:

	==1-methylpyrrole in complex with T4 Lysozyme L99A==		==1-methylpyrrole in complex with T4 Lysozyme L99A==
-	<StructureSection load='2ou0' size='340' side='right' caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='2ou0' size='340' side='right'caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MR3:1-METHYL-1H-PYRROLE'>MR3</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=MR3:1-METHYL-1H-PYRROLE'>MR3</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">[[181l\|181l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[181l\|181l]]</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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [~~http~~://pdbe.org/2ou0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ou0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ou0 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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [https://pdbe.org/2ou0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ou0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ou0 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/ou/2ou0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ou/2ou0_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 34:		Line 34:
	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-	*[[PDB identification code\|PDB identification code]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Graves, A P]]		[[Category: Graves, A P]]

OCA at 09:09, 18 October 2017

2017-10-18T09:09:16Z

←Older revision		Revision as of 09:09, 18 October 2017
Line 1:		Line 1:
		+
	==1-methylpyrrole in complex with T4 Lysozyme L99A==		==1-methylpyrrole in complex with T4 Lysozyme L99A==
	<StructureSection load='2ou0' size='340' side='right' caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2ou0' size='340' side='right' caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>
Line 7:		Line 8:
	<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 ([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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://pdbe.org/2ou0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://pdbe.org/2ou0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ou0 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=2ou0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:03, 11 September 2015

2015-09-11T16:03:12Z

←Older revision		Revision as of 16:03, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ou0' size='340' side='right' caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2ou0' size='340' side='right' caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MR3:1-METHYL-1H-PYRROLE'>MR3</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=MR3:1-METHYL-1H-PYRROLE'>MR3</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">[[181l\|181l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]]</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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://pdbe.org/2ou0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2ou0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Graves, A P]]		[[Category: Graves, A P]]

OCA at 18:45, 25 December 2014

2014-12-25T18:45:51Z

←Older revision		Revision as of 18:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MR3:1-METHYL-1H-PYRROLE'>MR3</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=MR3:1-METHYL-1H-PYRROLE'>MR3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]]</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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 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 37:		Line 39:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Graves, A P.]]	+	[[Category: Graves, A P]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Model system]]		[[Category: Model system]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 09:55, 29 September 2014

2014-09-29T09:55:03Z

←Older revision		Revision as of 09:55, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2ou0.~~png~~\|~~left~~\|200px]]	+	==1-methylpyrrole in complex with T4 Lysozyme L99A==
		+	<StructureSection load='2ou0' size='340' side='right' caption='[[2ou0]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ou0]] 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=2OU0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OU0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MR3:1-METHYL-1H-PYRROLE'>MR3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]]</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=2ou0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ou0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ou0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ou0 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/ou/2ou0_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 ==
		+	A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, beginning with single poses from docking, then including multiple poses, additional protein conformational changes, and using an improved charge model. Computed absolute binding free energies had an RMS error of 1.9 kcal/mol relative to previously determined experimental values. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys in a set of putative binders identified by docking. In these prospective tests, the RMS error in predicted binding free energies relative to those subsequently determined experimentally was only 0.6 kcal/mol. X-ray crystal structures of the new ligands bound in the cavity corresponded closely to predictions from the free energy calculations, but sometimes differed from those predicted by docking. Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved.

-	~~{{STRUCTURE_2ou0\| PDB=2ou0 \| SCENE= }}~~	+	Predicting absolute ligand binding free energies to a simple model site.,Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA J Mol Biol. 2007 Aug 24;371(4):1118-34. Epub 2007 Jun 8. PMID:17599350<ref>PMID:17599350</ref>

-	~~===1-methylpyrrole in complex with T4 Lysozyme L99A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17599350}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2ou0]] 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=2OU0 OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-		+	*[[PDB identification code\|PDB identification code]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:017599350<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 20:08, 20 October 2012

2012-10-20T20:08:58Z

←Older revision		Revision as of 20:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2ou0]] 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=2OU0 OCA].	+	[[2ou0]] 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=2OU0 OCA].

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

OCA: Protected "2ou0" [edit=sysop:move=sysop]

2012-07-27T09:33:59Z

Protected "2ou0" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:33, 27 July 2012

OCA at 09:33, 27 July 2012

2012-07-27T09:33:58Z

←Older revision		Revision as of 09:33, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ou0.png\|left\|200px]]		[[Image:2ou0.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ou0", 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_2ou0\| PDB=2ou0 \| SCENE= }}		{{STRUCTURE_2ou0\| PDB=2ou0 \| SCENE= }}

	===1-methylpyrrole in complex with T4 Lysozyme L99A===		===1-methylpyrrole in complex with T4 Lysozyme L99A===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17599350}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17599350 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17599350}}		{{ABSTRACT_PUBMED_17599350}}

	==About this Structure==		==About this Structure==
-	~~2OU0~~ 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=2OU0 OCA].	+	[[2ou0]] 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=2OU0 OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17599350~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017599350</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 31:		Line 22:
	[[Category: Model system]]		[[Category: Model system]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:54:54 2009''

OCA at 00:54, 18 February 2009

2009-02-18T00:54:55Z

←Older revision		Revision as of 00:54, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2OU0 is a ~~[[Single protein]]~~ 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=2OU0 OCA].	+	2OU0 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=2OU0 OCA].

	==Reference==		==Reference==
-	Predicting absolute ligand binding free energies to a simple model site., Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA, J Mol Biol. 2007 Aug 24;371(4):1118-34. Epub 2007 Jun 8. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17599350 17599350]~~	+	<ref group="xtra">PMID:17599350</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Single protein]]
	[[Category: Graves, A P.]]		[[Category: Graves, A P.]]
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
Line 33:		Line 32:
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 09~~:35:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:54:54 2009''