3g4w - Revision history

OCA at 06:59, 6 September 2023

OCA — Wed, 06 Sep 2023 06:59:29 GMT

←Older revision		Revision as of 06:59, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3g4w' size='340' side='right'caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3g4w' size='340' side='right'caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Anain Anain~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_inaequivalvis Anadara inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>~~, ~~<scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">HBI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])~~</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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [https://pdbe.org/3g4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [https://www.ebi.ac.uk/pdbsum/3g4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4w 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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [https://pdbe.org/3g4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [https://www.ebi.ac.uk/pdbsum/3g4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4w ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
	== 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: ~~Anain~~]]	+	[[Category: Anadara inaequivalvis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cohen, J]]	+	[[Category: Cohen J]]
-	[[Category: Gibson~~, Q H~~]]	+	[[Category: Gibson QH]]
-	[[Category: Knapp~~, J E~~]]	+	[[Category: Knapp JE]]
-	[[Category: Nichols~~, J C~~]]	+	[[Category: Nichols JC]]
-	[[Category: Pahl, R]]	+	[[Category: Pahl R]]
-	[[Category: Royer~~, W E~~]]	+	[[Category: Royer Jr WE]]
-	[[Category: Schulten, K]]	+	[[Category: Schulten K]]
-	[[Category: Srajer, V]]	+	[[Category: Srajer V]]
-	~~[[Category: Allostery]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxygen affinity]]~~	+
-	~~[[Category: Oxygen binding]]~~	+
-	~~[[Category: Oxygen storage/transport]]~~	+
-	~~[[Category: Oxygen transport~~]]	+

OCA at 07:55, 9 March 2022

OCA — Wed, 09 Mar 2022 07:55:46 GMT

←Older revision		Revision as of 07:55, 9 March 2022
Line 1:		Line 1:

	==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity==		==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity==
-	<StructureSection load='3g4w' size='340' side='right' caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3g4w' size='340' side='right'caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Anain Anain]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G4W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anain Anain]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])</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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [~~http~~://pdbe.org/3g4w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g4w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4w 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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [https://pdbe.org/3g4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [https://www.ebi.ac.uk/pdbsum/3g4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4w ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Anain]]		[[Category: Anain]]
		+	[[Category: Large Structures]]
	[[Category: Cohen, J]]		[[Category: Cohen, J]]
	[[Category: Gibson, Q H]]		[[Category: Gibson, Q H]]

OCA at 07:15, 5 December 2018

OCA — Wed, 05 Dec 2018 07:15:48 GMT

←Older revision		Revision as of 07:15, 5 December 2018
Line 1:		Line 1:
		+
	==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity==		==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity==
	<StructureSection load='3g4w' size='340' side='right' caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3g4w' size='340' side='right' caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])</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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://pdbe.org/3g4w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w 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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://pdbe.org/3g4w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4w ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/g4/3g4w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4w_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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	[[Category: Srajer, V]]		[[Category: Srajer, V]]
	[[Category: Allostery]]		[[Category: Allostery]]
		+	[[Category: Cytoplasm]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 03:54, 7 February 2016

OCA — Sun, 07 Feb 2016 03:54:56 GMT

←Older revision		Revision as of 03:54, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3g4w' size='340' side='right' caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3g4w' size='340' side='right' caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Scapharca_inaequivalvis Scapharca inaequivalvis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anain Anain]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ~~Scapharca inaequivalvis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])</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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w 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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://pdbe.org/3g4w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3g4w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3g4w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Scapharca inaequivalvis~~]]	+	[[Category: Anain]]
	[[Category: Cohen, J]]		[[Category: Cohen, J]]
	[[Category: Gibson, Q H]]		[[Category: Gibson, Q H]]

OCA at 08:50, 20 January 2015

OCA — Tue, 20 Jan 2015 08:50:03 GMT

←Older revision		Revision as of 08:50, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4W FirstGlance]. <br>		<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 Scapharca inaequivalvis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 Scapharca inaequivalvis])</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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w 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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Scapharca inaequivalvis]]		[[Category: Scapharca inaequivalvis]]
-	[[Category: Cohen, J.]]	+	[[Category: Cohen, J]]
-	[[Category: Gibson, Q H.]]	+	[[Category: Gibson, Q H]]
-	[[Category: Knapp, J E.]]	+	[[Category: Knapp, J E]]
-	[[Category: Nichols, J C.]]	+	[[Category: Nichols, J C]]
-	[[Category: Pahl, R.]]	+	[[Category: Pahl, R]]
-	[[Category: Royer, W E.]]	+	[[Category: Royer, W E]]
-	[[Category: Schulten, K.]]	+	[[Category: Schulten, K]]
-	[[Category: Srajer, V.]]	+	[[Category: Srajer, V]]
	[[Category: Allostery]]		[[Category: Allostery]]
	[[Category: Heme]]		[[Category: Heme]]

OCA at 11:25, 29 September 2014

OCA — Mon, 29 Sep 2014 11:25:07 GMT

←Older revision		Revision as of 11:25, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3g4w.~~png~~\|~~left~~\|200px]]	+	==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity==
		+	<StructureSection load='3g4w' size='340' side='right' caption='[[3g4w]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g4w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CL:CHLOROBENZENE'>8CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sdh\|3sdh]], [[3g46\|3g46]], [[3g4q\|3g4q]], [[3g4r\|3g4r]], [[3g4u\|3g4u]], [[3g4v\|3g4v]], [[3g4y\|3g4y]], [[3g52\|3g52]], [[3g53\|3g53]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 Scapharca inaequivalvis])</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=3g4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4w RCSB], [http://www.ebi.ac.uk/pdbsum/3g4w 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/g4/3g4w_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 ==
		+	As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.

-	~~{{STRUCTURE_3g4w\| PDB=3g4w \| SCENE= }}~~	+	Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.,Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE Jr Structure. 2009 Nov 11;17(11):1494-504. PMID:19913484<ref>PMID:19913484</ref>

-	~~===Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to~~ the ~~XE4 cavity===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19913484}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3g4w]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA].~~	+

	==See Also==		==See Also==
-	*[[Hemoglobin\|Hemoglobin]]	+	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019913484<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Scapharca inaequivalvis]]		[[Category: Scapharca inaequivalvis]]
	[[Category: Cohen, J.]]		[[Category: Cohen, J.]]

OCA at 05:31, 20 October 2012

OCA — Sat, 20 Oct 2012 05:31:24 GMT

←Older revision		Revision as of 05:31, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3g4w]] is a 2 chain structure ~~of [[Hemoglobin]]~~ with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA].	+	[[3g4w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA].

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

OCA: Protected "3g4w" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 10:19:50 GMT

Protected "3g4w" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:19, 25 July 2012

OCA at 10:19, 25 July 2012

OCA — Wed, 25 Jul 2012 10:19:47 GMT

←Older revision		Revision as of 10:19, 25 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3g4w.png\|left\|200px]]
-	[[Image:3g4w.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g4w", 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_3g4w\| PDB=3g4w \| SCENE= }}		{{STRUCTURE_3g4w\| PDB=3g4w \| SCENE= }}

	===Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity===		===Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19913484}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19913484 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19913484}}		{{ABSTRACT_PUBMED_19913484}}

	==About this Structure==		==About this Structure==
-	~~3G4W~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA].	+	[[3g4w]] is a 2 chain structure of [[Hemoglobin]] with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA].
		+
		+	==See Also==
		+	*[[Hemoglobin\|Hemoglobin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19913484~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019913484</ref><references group="xtra"/>
	[[Category: Scapharca inaequivalvis]]		[[Category: Scapharca inaequivalvis]]
	[[Category: Cohen, J.]]		[[Category: Cohen, J.]]
	[[Category: Gibson, Q H.]]		[[Category: Gibson, Q H.]]
-	[[Category: Jr., W E.Royer.]]
	[[Category: Knapp, J E.]]		[[Category: Knapp, J E.]]
	[[Category: Nichols, J C.]]		[[Category: Nichols, J C.]]
	[[Category: Pahl, R.]]		[[Category: Pahl, R.]]
		+	[[Category: Royer, W E.]]
	[[Category: Schulten, K.]]		[[Category: Schulten, K.]]
	[[Category: Srajer, V.]]		[[Category: Srajer, V.]]
	[[Category: Allostery]]		[[Category: Allostery]]
-	[[Category: Cytoplasm]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Iron]]		[[Category: Iron]]
Line 42:		Line 32:
	[[Category: Oxygen storage/transport]]		[[Category: Oxygen storage/transport]]
	[[Category: Oxygen transport]]		[[Category: Oxygen transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 2 09:50:39 2009''

OCA at 07:50, 2 December 2009

OCA — Wed, 02 Dec 2009 07:50:40 GMT

←Older revision		Revision as of 07:50, 2 December 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3g4w.jpg\|left\|200px]]

-	The ~~entry 3g4w~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3g4w", 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_3g4w\| PDB=3g4w \| SCENE= }}

-	~~Authors~~: ~~Knapp, J.E., Pahl, R., Cohen, J., Nichols, J.C., Schulten, K., Gibson, Q.H., Srajer, V., Royer Jr., W.E.~~	+	===Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity===

-	Description: Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chlorobenzene bound to the XE4 cavity

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar~~ ~~4 14~~:43:58 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19913484}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19913484 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19913484}}
		+
		+	==About this Structure==
		+	3G4W is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4W OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19913484</ref><references group="xtra"/>
		+	[[Category: Scapharca inaequivalvis]]
		+	[[Category: Cohen, J.]]
		+	[[Category: Gibson, Q H.]]
		+	[[Category: Jr., W E.Royer.]]
		+	[[Category: Knapp, J E.]]
		+	[[Category: Nichols, J C.]]
		+	[[Category: Pahl, R.]]
		+	[[Category: Schulten, K.]]
		+	[[Category: Srajer, V.]]
		+	[[Category: Allostery]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Heme]]
		+	[[Category: Iron]]
		+	[[Category: Metal-binding]]
		+	[[Category: Oxygen affinity]]
		+	[[Category: Oxygen binding]]
		+	[[Category: Oxygen storage/transport]]
		+	[[Category: Oxygen transport]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 2 09:50:39 2009''