2dds - Revision history

OCA at 00:51, 21 November 2024

2024-11-21T00:51:57Z

← Older revision		Revision as of 00:51, 21 November 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2dds_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2dds_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 11:37, 22 May 2024

2024-05-22T11:37:53Z

← Older revision		Revision as of 11:37, 22 May 2024
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	<StructureSection load='2dds' size='340' side='right'caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dds' size='340' side='right'caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_14579 Atcc 14579~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDS FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 1.8Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2ddr\|2ddr]], [[2ddt\|2ddt]]</div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12]~~ </~~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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [https://pdbe.org/2dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [https://www.ebi.ac.uk/pdbsum/2dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dds ProSAT], [https://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [https://pdbe.org/2dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [https://www.ebi.ac.uk/pdbsum/2dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dds ProSAT], [https://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).		[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 14579~~]]		[[Category: Bacillus cereus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Sphingomyelin phosphodiesterase]]~~		[[Category: Ago H]]
	[[Category: Ago, H]]		[[Category: Katunuma N]]
	[[Category: Katunuma, N]]		[[Category: Miyano M]]
	[[Category: Miyano, M]]		[[Category: Ochi S]]
	[[Category: Ochi, S]]		[[Category: Oda M]]
	[[Category: Oda, M]]		[[Category: Sakurai J]]
	~~[[Category: Structural genomic~~]]		[[Category: Takahashi M]]
	[[Category: Sakurai, J]]		[[Category: Tsuge H]]
	[[Category: Takahashi, M]]
	[[Category: Tsuge, H]]
	~~[[Category: Dnase i like folding]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Rsgi~~]]

OCA at 10:30, 8 December 2021

2021-12-08T10:30:16Z

← Older revision		Revision as of 10:30, 8 December 2021
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	<StructureSection load='2dds' size='340' side='right'caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dds' size='340' side='right'caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ddr\|2ddr]], [[2ddt\|2ddt]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [~~http~~://pdbe.org/2dds PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dds PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dds ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [https://pdbe.org/2dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [https://www.ebi.ac.uk/pdbsum/2dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dds ProSAT], [https://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).		[[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:34, 4 March 2020

2020-03-04T07:34:06Z

← Older revision		Revision as of 07:34, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion==		==Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion==
	<StructureSection load='2dds' size='340' side='right' caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dds' size='340' side='right'caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 14579]]		[[Category: Atcc 14579]]
			[[Category: Large Structures]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Ago, H]]		[[Category: Ago, H]]

OCA at 06:12, 30 May 2018

2018-05-30T06:12:45Z

← Older revision		Revision as of 06:12, 30 May 2018
Line 1:		Line 1:

	==Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion==		==Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion==
	<StructureSection load='2dds' size='340' side='right' caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dds' size='340' side='right' caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://pdbe.org/2dds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://pdbe.org/2dds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dds ProSAT], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2dds_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2dds_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>

OCA at 21:40, 9 February 2016

2016-02-09T21:40:51Z

← Older revision		Revision as of 21:40, 9 February 2016
Line 18:		Line 18:
	<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=2dds ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:17, 11 September 2015

2015-09-11T02:17:47Z

← Older revision		Revision as of 02:17, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2dds' size='340' side='right' caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dds' size='340' side='right' caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_cereus Bacillus cereus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://pdbe.org/2dds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2dds" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus cereus~~]]		[[Category: Atcc 14579]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Ago, H]]		[[Category: Ago, H]]

OCA at 09:43, 25 December 2014

2014-12-25T09:43:27Z

← Older revision		Revision as of 09:43, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Bacillus cereus]]		[[Category: Bacillus cereus]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Ago, H.]]		[[Category: Ago, H]]
	[[Category: Katunuma, N.]]		[[Category: Katunuma, N]]
	[[Category: Miyano, M.]]		[[Category: Miyano, M]]
	[[Category: Ochi, S.]]		[[Category: Ochi, S]]
	[[Category: Oda, M.]]		[[Category: Oda, M]]
	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]		[[Category: Structural genomic]]
	[[Category: Sakurai, J.]]		[[Category: Sakurai, J]]
	[[Category: Takahashi, M.]]		[[Category: Takahashi, M]]
	[[Category: Tsuge, H.]]		[[Category: Tsuge, H]]
	[[Category: Dnase i like folding]]		[[Category: Dnase i like folding]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	~~[[Category: Riken structural genomics/proteomics initiative]]~~
	[[Category: Rsgi]]		[[Category: Rsgi]]
	~~[[Category: Structural genomic]]~~

OCA at 05:00, 29 September 2014

2014-09-29T05:00:40Z

← Older revision		Revision as of 05:00, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2dds~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion==
			<StructureSection load='2dds' size='340' side='right' caption='[[2dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDS FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2ddt\|2ddt]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [http://www.ebi.ac.uk/pdbsum/2dds PDBsum], [http://www.topsan.org/Proteins/RSGI/2dds TOPSAN]</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/dd/2dds_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 ==
			Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin to phosphocholine and ceramide in a divalent metal ion-dependent manner. Bc-SMase is a homologue of mammalian neutral SMase (nSMase) and mimics the actions of the endogenous mammalian nSMase in causing differentiation, development, aging, and apoptosis. Thus Bc-SMase may be a good model for the poorly characterized mammalian nSMase. The metal ion activation of sphingomyelinase activity of Bc-SMase was in the order Co2+ > or = Mn2+ > or = Mg2+ >> Ca2+ > or = Sr2+. The first crystal structures of Bc-SMase bound to Co2+, Mg2+, or Ca2+ were determined. The water-bridged double divalent metal ions at the center of the cleft in both the Co2+- and Mg2+-bound forms were concluded to be the catalytic architecture required for sphingomyelinase activity. In contrast, the architecture of Ca2+ binding at the site showed only one binding site. A further single metal-binding site exists at one side edge of the cleft. Based on the highly conserved nature of the residues of the binding sites, the crystal structure of Bc-SMase with bound Mg2+ or Co2+ may provide a common structural framework applicable to phosphohydrolases belonging to the DNase I-like folding superfamily. In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate.

	~~{{STRUCTURE_2dds\| PDB=2dds \| SCENE= }}~~		Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.,Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J J Biol Chem. 2006 Jun 9;281(23):16157-67. Epub 2006 Apr 4. PMID:16595670<ref>PMID:16595670</ref>

	~~===Crystal structure~~ of ~~sphingomyelinase from Bacillus cereus with cobalt ion===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16595670}}~~

	~~==About this Structure==~~
	~~[[2dds]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_cereus Bacillus cereus]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2DDS OCA].~~

	==See Also==		==See Also==
	*[[Sphingomyelinase\|Sphingomyelinase]]		*[[Sphingomyelinase\|Sphingomyelinase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016595670<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Bacillus cereus]]		[[Category: Bacillus cereus]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]

OCA at 15:14, 20 October 2012

2012-10-20T15:14:21Z

← Older revision		Revision as of 15:14, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2dds]] is a 4 chain structure ~~of [[Sphingomyelinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA].		[[2dds]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA].

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