2ped - Revision history

OCA at 08:28, 30 October 2024

2024-10-30T08:28:19Z

← Older revision		Revision as of 08:28, 30 October 2024
Line 15:		Line 15:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/2ped_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/2ped_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 09:00, 25 October 2023

2023-10-25T09:00:41Z

← Older revision		Revision as of 09:00, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PED FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PED FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO~~</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN~~</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.95Å</td></tr>
	~~<tr id~~='~~NonStdRes'><td class~~=~~"sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res~~:~~]]</b~~></~~td><td class="sblockDat"~~><scene name='pdbligand=~~ACE~~:~~ACETYL+GROUP~~'>~~ACE~~</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1u19\|1u19]], [[2g87\|2g87]]~~</~~div~~></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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [https://pdbe.org/2ped PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [https://www.ebi.ac.uk/pdbsum/2ped PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped 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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [https://pdbe.org/2ped PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [https://www.ebi.ac.uk/pdbsum/2ped PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN]] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>		[https://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nakamichi, H]]		[[Category: Nakamichi H]]
	[[Category: Okada, T]]		[[Category: Okada T]]
	~~[[Category: G protein-coupled receptor]]~~
	~~[[Category: Rhodopsin]]~~
	~~[[Category: Signaling protein]]~~
	~~[[Category: Visual pigment~~]]

OCA at 07:45, 9 March 2022

2022-03-09T07:45:13Z

← Older revision		Revision as of 07:45, 9 March 2022
Line 3:		Line 3:
	<StructureSection load='2ped' size='340' side='right'caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='2ped' size='340' side='right'caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2PED FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PED FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~PLM~~:~~PALMITIC~~+~~ACID~~'>~~PLM~~</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL~~'>~~RET~~</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u19\|1u19]], [[2g87\|2g87]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [~~http~~://pdbe.org/2ped PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ped PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped 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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [https://pdbe.org/2ped PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [https://www.ebi.ac.uk/pdbsum/2ped PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN]] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>		[[https://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN]] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:54, 3 June 2020

2020-06-03T06:54:40Z

← Older revision		Revision as of 06:54, 3 June 2020
Line 1:		Line 1:

	==Crystallographic model of 9-cis-rhodopsin==		==Crystallographic model of 9-cis-rhodopsin==
	<StructureSection load='2ped' size='340' side='right' caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='2ped' size='340' side='right'caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PED FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2PED FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://pdbe.org/2ped PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://pdbe.org/2ped PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
	*[[Rhodopsin\|Rhodopsin]]		*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
			[[Category: Large Structures]]
	[[Category: Nakamichi, H]]		[[Category: Nakamichi, H]]
	[[Category: Okada, T]]		[[Category: Okada, T]]

OCA at 08:28, 29 August 2018

2018-08-29T08:28:51Z

← Older revision		Revision as of 08:28, 29 August 2018
Line 1:		Line 1:

	==Crystallographic model of 9-cis-rhodopsin==		==Crystallographic model of 9-cis-rhodopsin==
	<StructureSection load='2ped' size='340' side='right' caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='2ped' size='340' side='right' caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PED FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PED FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=~~PLM~~:~~PALMITIC+ACID~~'>~~PLM~~</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL~~'>~~RET~~</scene>, <scene name='pdbligand=ZN:~~ZINC~~+~~ION~~'>ZN</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://pdbe.org/2ped PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped 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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://pdbe.org/2ped PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/2ped_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/2ped_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 18:39, 9 February 2016

2016-02-09T18:39:56Z

← Older revision		Revision as of 18:39, 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=2ped ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:58, 11 September 2015

2015-09-11T00:58:43Z

← Older revision		Revision as of 00:58, 11 September 2015
Line 6:		Line 6:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped 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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://pdbe.org/2ped PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped PDBsum]</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 2ped" style="background-color:#fffaf0;"></div>

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

OCA at 08:44, 25 December 2014

2014-12-25T08:44:30Z

← Older revision		Revision as of 08:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PED FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PED FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped 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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN]] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Nakamichi, H.]]		[[Category: Nakamichi, H]]
	[[Category: Okada, T.]]		[[Category: Okada, T]]
	[[Category: G protein-coupled receptor]]		[[Category: G protein-coupled receptor]]
	[[Category: Rhodopsin]]		[[Category: Rhodopsin]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]
	[[Category: Visual pigment]]		[[Category: Visual pigment]]

OCA at 09:45, 29 September 2014

2014-09-29T09:45:49Z

← Older revision		Revision as of 09:45, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2ped~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystallographic model of 9-cis-rhodopsin==
			<StructureSection load='2ped' size='340' side='right' caption='[[2ped]], [[Resolution\|resolution]] 2.95Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PED FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u19\|1u19]], [[2g87\|2g87]]</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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [http://www.ebi.ac.uk/pdbsum/2ped 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/pe/2ped_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 ==
			The primary photochemical process of the visual function has been investigated using the three crystallographic models, 11-cis-rhodopsin, all-trans-bathorhodopsin, and the artificial isomeric 9-cis-rhodopsin. Detailed examination of the atomic displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency.

	~~{{STRUCTURE_2ped\| PDB=2ped \| SCENE= }}~~		Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography.,Nakamichi H, Buss V, Okada T Biophys J. 2007 Jun 15;92(12):L106-8. Epub 2007 Apr 20. PMID:17449675<ref>PMID:17449675</ref>

	~~===Crystallographic model~~ of ~~9-cis-rhodopsin===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17449675}}~~

	~~==About this Structure==~~
	~~[[2ped]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bos_taurus Bos taurus]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2PED OCA].~~

	==See Also==		==See Also==
	*[[Rhodopsin\|Rhodopsin]]		*[[Rhodopsin\|Rhodopsin]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:017449675<~~/~~ref~~><~~ref group="xtra">PMID:017263385</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Nakamichi, H.]]		[[Category: Nakamichi, H.]]

OCA at 14:46, 20 October 2012

2012-10-20T14:46:05Z

← Older revision		Revision as of 14:46, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2ped]] is a 2 chain structure ~~of [[Rhodopsin]]~~ with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA].		[[2ped]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA].

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