2rb2 - Revision history

OCA at 09:21, 21 February 2024

2024-02-21T09:21:18Z

← Older revision		Revision as of 09:21, 21 February 2024
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	<StructureSection load='2rb2' size='340' side='right'caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='2rb2' size='340' side='right'caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=263:1-(AZIDOMETHYL)-3~~-~~METHYLBENZENE'>263</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]] 1.463Å</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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [https://pdbe.org/2rb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb2 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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [https://pdbe.org/2rb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/~~LYS_BPT4 LYS_BPT4~~]~~] Helps~~ to ~~release~~ the mature ~~phage~~ particles ~~from~~ the cell ~~wall by breaking~~ down the peptidoglycan.		[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2rb2 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=2rb2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<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.

	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>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2rb2" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__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

2021-07-02T04:20:13Z

← Older revision		Revision as of 04:20, 2 July 2021
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	==3-methylbenzylazide in complex with T4 lysozyme L99A==		==3-methylbenzylazide in complex with T4 lysozyme L99A==
	<StructureSection load='2rb2' size='340' side='right' caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='2rb2' size='340' side='right'caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [~~http~~://pdbe.org/2rb2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb2 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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [https://pdbe.org/2rb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb2 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/rb/2rb2_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rb2_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>
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	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
			[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]

OCA at 07:47, 25 October 2017

2017-10-25T07:47:06Z

← Older revision		Revision as of 07:47, 25 October 2017
Line 1:		Line 1:

	==3-methylbenzylazide in complex with T4 lysozyme L99A==		==3-methylbenzylazide in complex with T4 lysozyme L99A==
	<StructureSection load='2rb2' size='340' side='right' caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='2rb2' size='340' side='right' caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>
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	<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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://pdbe.org/2rb2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://pdbe.org/2rb2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:41, 10 February 2016

2016-02-10T04:41:23Z

← Older revision		Revision as of 04:41, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='2rb2' size='340' side='right' caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='2rb2' size='340' side='right' caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://pdbe.org/2rb2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=2rb2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 2rb2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Enterobacteria phage t4~~]]		[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]

OCA at 11:51, 25 December 2014

2014-12-25T11:51:27Z

← Older revision		Revision as of 11:51, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 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: 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 07:43, 29 September 2014

2014-09-29T07:43:46Z

← Older revision		Revision as of 07:43, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2rb2~~.~~png~~\|~~left~~\|~~200px~~]]		==3-methylbenzylazide in complex with T4 lysozyme L99A==
			<StructureSection load='2rb2' size='340' side='right' caption='[[2rb2]], [[Resolution\|resolution]] 1.46Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2rb2]] 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=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</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]], [[2rbn\|2rbn]], [[2rbo\|2rbo]], [[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=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb2 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/rb/2rb2_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 ==
			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_2rb2\| PDB=2rb2 \| 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>

	~~===3-methylbenzylazide in complex with T4 lysozyme L99A===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18280498}}~~

	~~==About this Structure==~~
	~~[[2rb2]] 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=2RB2 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 16:22, 20 October 2012

2012-10-20T16:22:03Z

← Older revision		Revision as of 16:22, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2rb2]] 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=2RB2 OCA].		[[2rb2]] 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=2RB2 OCA].

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

OCA: Protected "2rb2" [edit=sysop:move=sysop]

2012-07-26T21:26:18Z

Protected "2rb2" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:26, 26 July 2012
(No difference)

OCA at 21:26, 26 July 2012

2012-07-26T21:26:16Z

← Older revision		Revision as of 21:26, 26 July 2012
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	~~{{Seed}}~~
	[[Image:2rb2.png\|left\|200px]]		[[Image:2rb2.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2rb2", 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_2rb2\| PDB=2rb2 \| SCENE= }}		{{STRUCTURE_2rb2\| PDB=2rb2 \| SCENE= }}

	===3-methylbenzylazide in complex with T4 lysozyme L99A===		===3-methylbenzylazide in complex with T4 lysozyme L99A===


	~~<!--~~
	~~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==
	~~2RB2~~ 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=2RB2 OCA].		[[2rb2]] 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=2RB2 OCA].

			==See Also==
			*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18280498~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018280498</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 31:		Line 22:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Protein cavity]]		[[Category: Protein cavity]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:30:39 2009''~~

OCA at 13:30, 17 February 2009

2009-02-17T13:30:42Z

← Older revision		Revision as of 13:30, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2RB2 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=2RB2 OCA].		2RB2 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=2RB2 OCA].

	==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:18280498</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.]]
Line 33:		Line 32:
	[[Category: Protein cavity]]		[[Category: Protein cavity]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 21~~:11:~~26 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:30:39 2009''