3cod - Revision history

OCA at 19:11, 20 October 2021

2021-10-20T19:11:58Z

←Older revision		Revision as of 19:11, 20 October 2021
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	==Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin==		==Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin==
-	<StructureSection load='3cod' size='340' side='right' caption='[[3cod]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3cod' size='340' side='right'caption='[[3cod]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3COD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3COD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 "Bacillus halobius ruber" Klebahn 1919])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 "Bacillus halobius ruber" Klebahn 1919])</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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [~~http~~://pdbe.org/3cod PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3cod PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3cod 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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [https://pdbe.org/3cod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [https://www.ebi.ac.uk/pdbsum/3cod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cod ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.	+	[[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/co/3cod_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/co/3cod_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>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3cod" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3cod" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus halobius ruber klebahn 1919]]		[[Category: Bacillus halobius ruber klebahn 1919]]
		+	[[Category: Large Structures]]
	[[Category: Bowie, J U]]		[[Category: Bowie, J U]]
	[[Category: Faham, S]]		[[Category: Faham, S]]

OCA at 08:31, 25 October 2017

2017-10-25T08:31:46Z

←Older revision		Revision as of 08:31, 25 October 2017
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	</div>		</div>
	<div class="pdbe-citations 3cod" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3cod" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:02, 5 August 2016

2016-08-05T23:02:04Z

←Older revision		Revision as of 23:02, 5 August 2016
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		+
	==Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin==		==Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin==
	<StructureSection load='3cod' size='340' side='right' caption='[[3cod]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3cod' size='340' side='right' caption='[[3cod]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Halobacterium_salinarum Halobacterium salinarum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 ~~Halobacterium salinarum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 "Bacillus halobius ruber" Klebahn 1919])</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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [http://www.ebi.ac.uk/pdbsum/3cod 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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [http://pdbe.org/3cod PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [http://www.ebi.ac.uk/pdbsum/3cod PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cod ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=3cod 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 3cod" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halobacterium salinarum~~]]	+	[[Category: Bacillus halobius ruber klebahn 1919]]
	[[Category: Bowie, J U]]		[[Category: Bowie, J U]]
	[[Category: Faham, S]]		[[Category: Faham, S]]

OCA at 22:41, 25 December 2014

2014-12-25T22:41:36Z

←Older revision		Revision as of 22:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 Halobacterium salinarum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 Halobacterium salinarum])</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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [http://www.ebi.ac.uk/pdbsum/3cod 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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [http://www.ebi.ac.uk/pdbsum/3cod PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
	== 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: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
-	[[Category: Bowie, J U.]]	+	[[Category: Bowie, J U]]
-	[[Category: Faham, S.]]	+	[[Category: Faham, S]]
-	[[Category: Joh, N H.]]	+	[[Category: Joh, N H]]
-	[[Category: Min, A.]]	+	[[Category: Min, A]]
	[[Category: Chromophore]]		[[Category: Chromophore]]
	[[Category: Hydrogen bond]]		[[Category: Hydrogen bond]]

OCA at 10:08, 29 September 2014

2014-09-29T10:08:05Z

←Older revision		Revision as of 10:08, 29 September 2014
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-	[[~~Image:~~3cod.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin==
		+	<StructureSection load='3cod' size='340' side='right' caption='[[3cod]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3cod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1py6\|1py6]], [[1xji\|1xji]], [[3coc\|3coc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2242 Halobacterium salinarum])</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=3cod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cod RCSB], [http://www.ebi.ac.uk/pdbsum/3cod 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/co/3cod_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 ==
		+	Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.

-	~~{{STRUCTURE_3cod\| PDB=3cod \| SCENE= }}~~	+	Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins.,Joh NH, Min A, Faham S, Whitelegge JP, Yang D, Woods VL, Bowie JU Nature. 2008 Jun 26;453(7199):1266-70. Epub 2008 May 25. PMID:18500332<ref>PMID:18500332</ref>

-	~~===Crystal Structure of T90A~~/~~D115A mutant~~ of ~~Bacteriorhodopsin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18500332}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3cod]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Halobacterium_salinarum Halobacterium salinarum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].~~	+

	==See Also==		==See Also==
	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]		*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018500332<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Bowie, J U.]]		[[Category: Bowie, J U.]]

OCA at 22:30, 20 October 2012

2012-10-20T22:30:30Z

←Older revision		Revision as of 22:30, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3cod]] is a 2 chain structure ~~of [[Bacteriorhodopsin]]~~ with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].	+	[[3cod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].

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

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

2012-07-27T16:32:29Z

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

←Older revision

Revision as of 16:32, 27 July 2012

OCA at 16:32, 27 July 2012

2012-07-27T16:32:26Z

←Older revision		Revision as of 16:32, 27 July 2012
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-	{{Seed}}
	[[Image:3cod.png\|left\|200px]]		[[Image:3cod.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3cod", 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_3cod\| PDB=3cod \| SCENE= }}		{{STRUCTURE_3cod\| PDB=3cod \| SCENE= }}

	===Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin===		===Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18500332}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18500332 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18500332}}		{{ABSTRACT_PUBMED_18500332}}

	==About this Structure==		==About this Structure==
-	~~3COD~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].	+	[[3cod]] is a 2 chain structure of [[Bacteriorhodopsin]] with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18500332~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018500332</ref><references group="xtra"/>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Bowie, J U.]]		[[Category: Bowie, J U.]]
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	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport]]		[[Category: Transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 10:00:35 2009''

OCA at 08:00, 18 February 2009

2009-02-18T08:00:36Z

←Older revision		Revision as of 08:00, 18 February 2009
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	==About this Structure==		==About this Structure==
-	3COD is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].	+	3COD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COD OCA].

	==Reference==		==Reference==
-	~~Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins., Joh NH, Min A, Faham S, Whitelegge JP, Yang D, Woods VL, Bowie JU, Nature. 2008 May 25;.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18500332 18500332]~~	+	<ref group="xtra">PMID:18500332</ref><references group="xtra"/>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
-	[[Category: Single protein]]
	[[Category: Bowie, J U.]]		[[Category: Bowie, J U.]]
	[[Category: Faham, S.]]		[[Category: Faham, S.]]
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	[[Category: Transport]]		[[Category: Transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 9~~ 10:11:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 10:00:35 2009''

OCA at 07:11, 9 July 2008

2008-07-09T07:11:18Z

←Older revision		Revision as of 07:11, 9 July 2008
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-	[[Image:3cod.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3cod.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3cod\| PDB=3cod \| SCENE= }}		{{STRUCTURE_3cod\| PDB=3cod \| SCENE= }}

-	~~'''~~Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin~~'''~~	+	===Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin===


-	~~==Overview==~~	+	<!--
-	~~Understanding~~ the ~~energetics of molecular interactions is fundamental~~ to ~~all of~~ the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as ~~an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water~~. ~~Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins~~. ~~Because of limited structural information and technical challenges~~, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is ~~only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in~~ the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. ~~Our results indicate that most hydrogen~~-~~bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen~~-~~bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18500332}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18500332 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18500332}}

	==About this Structure==		==About this Structure==
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	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport]]		[[Category: Transport]]
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