2rbo - Revision history

OCA at 13:11, 26 July 2023

OCA — Wed, 26 Jul 2023 13:11:01 GMT

←Older revision		Revision as of 13:11, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='2rbo' size='340' side='right'caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>		<StructureSection load='2rbo' size='340' side='right'caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=265:2~~-~~NITROTHIOPHENE'>265</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;'>[[181l\|181l]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=265:2-NITROTHIOPHENE'>265</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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [https://pdbe.org/2rbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [https://www.ebi.ac.uk/pdbsum/2rbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbo 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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [https://pdbe.org/2rbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [https://www.ebi.ac.uk/pdbsum/2rbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbo 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__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: Graves AP]]
-	[[Category: Graves~~, A P~~]]	+	[[Category: Shoichet BK]]
-	[[Category: Shoichet~~, B K]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein cavity~~]]	+

OCA at 04:20, 2 July 2021

OCA — Fri, 02 Jul 2021 04:20:48 GMT

←Older revision		Revision as of 04:20, 2 July 2021
Line 1:		Line 1:

	==2-nitrothiophene in complex with T4 lysozyme L99A/M102Q==		==2-nitrothiophene in complex with T4 lysozyme L99A/M102Q==
-	<StructureSection load='2rbo' size='340' side='right' caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>	+	<StructureSection load='2rbo' size='340' side='right'caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RBO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=265:2-NITROTHIOPHENE'>265</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=265:2-NITROTHIOPHENE'>265</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]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</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]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [~~http~~://pdbe.org/2rbo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rbo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbo 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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [https://pdbe.org/2rbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [https://www.ebi.ac.uk/pdbsum/2rbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbo 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]

OCA at 07:20, 5 August 2016

OCA — Fri, 05 Aug 2016 07:20:57 GMT

←Older revision		Revision as of 07:20, 5 August 2016
Line 1:		Line 1:
		+
	==2-nitrothiophene in complex with T4 lysozyme L99A/M102Q==		==2-nitrothiophene in complex with T4 lysozyme L99A/M102Q==
	<StructureSection load='2rbo' size='340' side='right' caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>		<StructureSection load='2rbo' size='340' side='right' caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=265:2-NITROTHIOPHENE'>265</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=265:2-NITROTHIOPHENE'>265</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]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [http://www.ebi.ac.uk/pdbsum/2rbo 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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [http://pdbe.org/2rbo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [http://www.ebi.ac.uk/pdbsum/2rbo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 2rbo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]

OCA at 00:13, 25 December 2014

OCA — Thu, 25 Dec 2014 00:13:03 GMT

←Older revision		Revision as of 00:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=265:2-NITROTHIOPHENE'>265</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=265:2-NITROTHIOPHENE'>265</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]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [http://www.ebi.ac.uk/pdbsum/2rbo 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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [http://www.ebi.ac.uk/pdbsum/2rbo 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Boyce, S E.]]	+	[[Category: Boyce, S E]]
-	[[Category: Graves, A P.]]	+	[[Category: Graves, A P]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Protein cavity]]		[[Category: Protein cavity]]

OCA at 00:53, 2 October 2014

OCA — Thu, 02 Oct 2014 00:53:49 GMT

←Older revision		Revision as of 00:53, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2rbo.~~png~~\|~~left~~\|~~200px~~]]	+	==2-nitrothiophene in complex with T4 lysozyme L99A/M102Q==
		+	<StructureSection load='2rbo' size='340' side='right' caption='[[2rbo]], [[Resolution\|resolution]] 1.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rbo]] 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=2RBO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=265:2-NITROTHIOPHENE'>265</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]], [[1lgu\|1lgu]], [[2ray\|2ray]], [[2raz\|2raz]], [[2rb0\|2rb0]], [[2rb1\|2rb1]], [[2rb2\|2rb2]], [[2rbn\|2rbn]], [[2rbp\|2rbp]], [[2rbq\|2rbq]], [[2rbr\|2rbr]], [[2ras\|2ras]]</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=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbo RCSB], [http://www.ebi.ac.uk/pdbsum/2rbo PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Molecular docking computationally screens thousands to millions of organic molecules against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low "hit rates." A strategy to overcome these approximations is to rescore top-ranked docked molecules using a better but slower method. One such is afforded by molecular mechanics-generalized Born surface area (MM-GBSA) techniques. These more physically realistic methods have improved models for solvation and electrostatic interactions and conformational change compared to most docking programs. To investigate MM-GBSA rescoring, we re-ranked docking hit lists in three small buried sites: a hydrophobic cavity that binds apolar ligands, a slightly polar cavity that binds aryl and hydrogen-bonding ligands, and an anionic cavity that binds cationic ligands. These sites are simple; consequently, incorrect predictions can be attributed to particular errors in the method, and many likely ligands may actually be tested. In retrospective calculations, MM-GBSA techniques with binding-site minimization better distinguished the known ligands for each cavity from the known decoys compared to the docking calculation alone. This encouraged us to test rescoring prospectively on molecules that ranked poorly by docking but that ranked well when rescored by MM-GBSA. A total of 33 molecules highly ranked by MM-GBSA for the three cavities were tested experimentally. Of these, 23 were observed to bind--these are docking false negatives rescued by rescoring. The 10 remaining molecules are true negatives by docking and false positives by MM-GBSA. X-ray crystal structures were determined for 21 of these 23 molecules. In many cases, the geometry prediction by MM-GBSA improved the initial docking pose and more closely resembled the crystallographic result; yet in several cases, the rescored geometry failed to capture large conformational changes in the protein. Intriguingly, rescoring not only rescued docking false positives, but also introduced several new false positives into the top-ranking molecules. We consider the origins of the successes and failures in MM-GBSA rescoring in these model cavity sites and the prospects for rescoring in biologically relevant targets.

-	~~{{STRUCTURE_2rbo\| PDB=2rbo \| SCENE= }}~~	+	Rescoring docking hit lists for model cavity sites: predictions and experimental testing.,Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK J Mol Biol. 2008 Mar 28;377(3):914-34. Epub 2008 Jan 30. PMID:18280498<ref>PMID:18280498</ref>

-	~~===2-nitrothiophene in complex with T4 lysozyme L99A~~/~~M102Q===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18280498}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2rbo]] 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=2RBO 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:018280498<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 10:32, 20 October 2012

OCA — Sat, 20 Oct 2012 10:32:54 GMT

←Older revision		Revision as of 10:32, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2rbo]] 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=2RBO OCA].	+	[[2rbo]] 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=2RBO OCA].

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

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

OCA — Thu, 26 Jul 2012 02:28:34 GMT

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

←Older revision

Revision as of 02:28, 26 July 2012

OCA at 02:28, 26 July 2012

OCA — Thu, 26 Jul 2012 02:28:33 GMT

←Older revision		Revision as of 02:28, 26 July 2012
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-	{{Seed}}
	[[Image:2rbo.png\|left\|200px]]		[[Image:2rbo.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rbo", 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_2rbo\| PDB=2rbo \| SCENE= }}		{{STRUCTURE_2rbo\| PDB=2rbo \| SCENE= }}

	===2-nitrothiophene in complex with T4 lysozyme L99A/M102Q===		===2-nitrothiophene in complex with T4 lysozyme L99A/M102Q===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18280498}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18280498 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18280498}}		{{ABSTRACT_PUBMED_18280498}}

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

	==Reference==		==Reference==
-	Rescoring docking hit lists for model cavity sites: predictions and experimental testing., Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK, J Mol Biol. 2008 Mar 28;377(3):914-34. Epub 2008 Jan 30. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~18280498 18280498]~~	+	<ref group="xtra">PMID:018280498</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Single protein]]
	[[Category: Boyce, S E.]]		[[Category: Boyce, S E.]]
	[[Category: Graves, A P.]]		[[Category: Graves, A P.]]
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	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Protein cavity]]		[[Category: Protein cavity]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:12:21 2008''

OCA at 01:12, 28 July 2008

OCA — Mon, 28 Jul 2008 01:12:24 GMT

←Older revision		Revision as of 01:12, 28 July 2008
Line 1:		Line 1:
-	[[Image:2rbo.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2rbo.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2rbo\| PDB=2rbo \| SCENE= }}		{{STRUCTURE_2rbo\| PDB=2rbo \| SCENE= }}

-	~~'''~~2-nitrothiophene in complex with T4 lysozyme L99A/M102Q~~'''~~	+	===2-nitrothiophene in complex with T4 lysozyme L99A/M102Q===


-	~~==Overview==~~	+	<!--
-	Molecular docking computationally screens thousands to millions of organic molecules against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low "hit rates." A strategy to overcome these approximations is to rescore top-~~ranked docked molecules using a better but slower method. One such is afforded by molecular mechanics~~-generalized Born surface area (MM-GBSA) techniques. These more physically realistic methods have improved models for solvation and electrostatic interactions and conformational change compared to most docking programs. To investigate MM-GBSA rescoring, ~~we re-ranked docking hit lists in three small buried sites: a hydrophobic cavity that binds apolar ligands~~, a slightly polar cavity that binds aryl and hydrogen-bonding ligands, and an anionic cavity that binds cationic ligands. These sites are simple; consequently, incorrect predictions can be attributed to particular errors in the method, and many likely ligands may actually be tested. In retrospective calculations, MM-GBSA techniques with binding-site minimization better distinguished the known ligands for each cavity from the ~~known decoys compared~~ to the ~~docking calculation alone. This encouraged us to test rescoring prospectively~~ on ~~molecules that ranked poorly by docking but that ranked well when rescored by MM-GBSA~~. ~~A total of 33 molecules highly ranked by MM-GBSA for the three cavities were tested experimentally~~. Of these, 23 were observed to bind--these are docking false negatives rescued by rescoring. The 10 remaining molecules are true negatives by docking and false positives by MM-GBSA. X-ray crystal structures were determined for 21 of these 23 molecules. In many cases, the geometry prediction by MM-GBSA improved the initial docking pose and more closely resembled the crystallographic result; yet in several cases, the rescored geometry failed to capture large conformational changes in the protein. ~~Intriguingly, rescoring not only rescued docking false positives, but also introduced several new false positives into the top~~-~~ranking molecules. We consider the origins of the successes and failures in MM~~-~~GBSA rescoring in these model cavity sites and the prospects for rescoring in biologically relevant targets.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18280498}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18280498 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18280498}}

	==About this Structure==		==About this Structure==
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	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Protein cavity]]		[[Category: Protein cavity]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 24 09:~~28:27 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:12:21 2008''

OCA at 06:28, 24 April 2008

OCA — Thu, 24 Apr 2008 06:28:28 GMT

←Older revision		Revision as of 06:28, 24 April 2008
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	[[Image:2rbo.jpg\|left\|200px]]		[[Image:2rbo.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 2rbo \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>2rbo</scene>, resolution 1.29Å~~	+	The line below this paragraph, containing "STRUCTURE_2rbo", creates the "Structure Box" on the page.
-	~~\|SITE= <scene name='pdbsite=AC1:Po4+Binding+Site+For+Residue+A+2001'>AC1</scene> and <scene name='pdbsite=AC2:265+Binding+Site+For+Residue+A+1001'>AC2</scene>~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=265:2~~-~~NITROTHIOPHENE'>265</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <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>~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= E~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]~~)	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_2rbo\| PDB=2rbo \| SCENE= }}
-	~~\|RELATEDENTRY=[[181l\|181L]]~~, ~~[[1lgu\|1LGU]], [[2ray\|2RAY]], [[2raz\|2RAZ]], [[2rb0\|2RB0]], [[2rb1\|2RB1]], [[2rb2\|2RB2]], [[2rbn\|2RBN]], [[2rbp\|2RBP]], [[2rbq\|2RBQ]], [[2rbr\|2RBR]], [[2ras\|2RAS]]~~	+
-	~~\|RESOURCES=<span class='plainlinks'>[http://oca~~.~~weizmann.ac.il/oca~~-~~docs/fgij/fg.htm?mol=2rbo FirstGlance], [http://oca.weizmann.ac.il/oca~~-~~bin/ocaids?id~~=2rbo ~~OCA], [http://www.ebi.ac.uk/pdbsum/2rbo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId~~=~~2rbo RCSB]</span>~~	+
-	}}	+

	'''2-nitrothiophene in complex with T4 lysozyme L99A/M102Q'''		'''2-nitrothiophene in complex with T4 lysozyme L99A/M102Q'''
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	[[Category: Graves, A P.]]		[[Category: Graves, A P.]]
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
-	[[Category: ~~hydrolase~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~protein~~ cavity]]	+	[[Category: Protein cavity]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:28:27 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 04~~:58:36 2008''	+