2d2n - Revision history

OCA at 07:50, 23 October 2024

2024-10-23T07:50:30Z

← Older revision		Revision as of 07:50, 23 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/2d2n_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/2d2n_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 11:33, 22 May 2024

2024-05-22T11:33:44Z

← Older revision		Revision as of 11:33, 22 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 3.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2m\|2d2m]]</div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [https://pdbe.org/2d2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [https://www.ebi.ac.uk/pdbsum/2d2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2n 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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [https://pdbe.org/2d2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [https://www.ebi.ac.uk/pdbsum/2d2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	~~[[https://www.uniprot.org/uniprot/GLBB1_OLIMA GLBB1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and sulfide simultaneously and reversibly at two different sites. [~~[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBB2_OLIMA GLBB2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBA2_OLIMA GLBA2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.		[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oligobrachia mashikoi]]		[[Category: Oligobrachia mashikoi]]
	[[Category: Fukumori, Y]]		[[Category: Fukumori Y]]
	[[Category: Kita, A]]		[[Category: Kita A]]
	[[Category: Miki, K]]		[[Category: Miki K]]
	[[Category: Nakagawa, T]]		[[Category: Nakagawa T]]
	[[Category: Numoto, N]]		[[Category: Numoto N]]
	[[Category: Sasayama, Y]]		[[Category: Sasayama Y]]
	~~[[Category: Giant hemoglobin]]~~
	~~[[Category: Invertebrate]]~~
	~~[[Category: Oxygen storage-transport complex]]~~
	~~[[Category: Pogonophora]]~~
	~~[[Category: Sulfide binding~~]]

OCA at 10:26, 8 December 2021

2021-12-08T10:26:19Z

← Older revision		Revision as of 10:26, 8 December 2021
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	<StructureSection load='2d2n' size='340' side='right'caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2d2n' size='340' side='right'caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D2N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2m\|2d2m]]</div></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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [~~http~~://pdbe.org/2d2n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d2n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2n 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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [https://pdbe.org/2d2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [https://www.ebi.ac.uk/pdbsum/2d2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/GLBB1_OLIMA GLBB1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and sulfide simultaneously and reversibly at two different sites. [[~~http~~://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[~~http~~://www.uniprot.org/uniprot/GLBB2_OLIMA GLBB2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[~~http~~://www.uniprot.org/uniprot/GLBA2_OLIMA GLBA2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.		[[https://www.uniprot.org/uniprot/GLBB1_OLIMA GLBB1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and sulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBB2_OLIMA GLBB2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBA2_OLIMA GLBA2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:58, 4 March 2020

2020-03-04T07:58:45Z

← Older revision		Revision as of 07:58, 4 March 2020
Line 1:		Line 1:

	==Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi==		==Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi==
	<StructureSection load='2d2n' size='340' side='right' caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2d2n' size='340' side='right'caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D2N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D2N FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Oligobrachia mashikoi]]		[[Category: Oligobrachia mashikoi]]
	[[Category: Fukumori, Y]]		[[Category: Fukumori, Y]]

OCA at 06:53, 30 May 2018

2018-05-30T06:53:11Z

← Older revision		Revision as of 06:53, 30 May 2018
Line 1:		Line 1:

	==Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi==		==Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi==
	<StructureSection load='2d2n' size='340' side='right' caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2d2n' size='340' side='right' caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://pdbe.org/2d2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n 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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://pdbe.org/2d2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2n ProSAT]</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/d2/2d2n_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/2d2n_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 15:53, 7 February 2016

2016-02-07T15:53:18Z

← Older revision		Revision as of 15:53, 7 February 2016
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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=2d2n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:58, 10 September 2015

2015-09-10T02:58:00Z

← Older revision		Revision as of 02:58, 10 September 2015
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n 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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://pdbe.org/2d2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~GLBB_OLIMA GLBB_OLIMA~~]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/~~GLBC_OLIMA GLBC_OLIMA~~]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/~~GLB5_OLIMA GLB5_OLIMA~~]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.		[[http://www.uniprot.org/uniprot/GLBB1_OLIMA GLBB1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and sulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBB2_OLIMA GLBB2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBA2_OLIMA GLBA2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 2d2n" style="background-color:#fffaf0;"></div>

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

OCA at 16:26, 24 December 2014

2014-12-24T16:26:39Z

← Older revision		Revision as of 16:26, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D2N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D2N FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n 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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/GLBB_OLIMA GLBB_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBC_OLIMA GLBC_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLB5_OLIMA GLB5_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Oligobrachia mashikoi]]		[[Category: Oligobrachia mashikoi]]
	[[Category: Fukumori, Y.]]		[[Category: Fukumori, Y]]
	[[Category: Kita, A.]]		[[Category: Kita, A]]
	[[Category: Miki, K.]]		[[Category: Miki, K]]
	[[Category: Nakagawa, T.]]		[[Category: Nakagawa, T]]
	[[Category: Numoto, N.]]		[[Category: Numoto, N]]
	[[Category: Sasayama, Y.]]		[[Category: Sasayama, Y]]
	[[Category: Giant hemoglobin]]		[[Category: Giant hemoglobin]]
	[[Category: Invertebrate]]		[[Category: Invertebrate]]
	~~[[Category: Oligobrachia mashikoi]]~~
	[[Category: Oxygen storage-transport complex]]		[[Category: Oxygen storage-transport complex]]
	[[Category: Pogonophora]]		[[Category: Pogonophora]]
	[[Category: Sulfide binding]]		[[Category: Sulfide binding]]

OCA at 05:59, 29 September 2014

2014-09-29T05:59:23Z

← Older revision		Revision as of 05:59, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2d2n~~.~~png~~\|~~left~~\|~~200px~~]]		==Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi==
			<StructureSection load='2d2n' size='340' side='right' caption='[[2d2n]], [[Resolution\|resolution]] 3.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2d2n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D2N FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MMC:METHYL+MERCURY+ION'>MMC</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2m\|2d2m]]</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=2d2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d2n RCSB], [http://www.ebi.ac.uk/pdbsum/2d2n 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/d2/2d2n_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 ==
			Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.

	~~{{STRUCTURE_2d2n\| PDB=2d2n \| SCENE= }}~~		Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.,Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14521-6. Epub 2005 Oct 3. PMID:16204001<ref>PMID:16204001</ref>

	~~===Structure of an extracellular giant hemoglobin~~ of the ~~gutless beard worm Oligobrachia mashikoi===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16204001}}~~

	~~==About this Structure==~~
	~~[[2d2n]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA].~~

	==See Also==		==See Also==
	*[[Hemoglobin\|Hemoglobin]]		*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016204001<~~/~~ref~~><~~ref group="xtra">PMID:015951254</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Oligobrachia mashikoi]]		[[Category: Oligobrachia mashikoi]]
	[[Category: Fukumori, Y.]]		[[Category: Fukumori, Y.]]

OCA at 07:08, 20 October 2012

2012-10-20T07:08:19Z

← Older revision		Revision as of 07:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2d2n]] is a 4 chain structure ~~of [[Hemoglobin]]~~ with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA].		[[2d2n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2N OCA].

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