1rul - Revision history

OCA at 06:08, 23 August 2023

OCA — Wed, 23 Aug 2023 06:08:25 GMT

←Older revision		Revision as of 06:08, 23 August 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RUL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.88Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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;~~'>~~[[1ncw\|1ncw]], [[1nd0\|1nd0]], [[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]~~</~~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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [https://pdbe.org/1rul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [https://www.ebi.ac.uk/pdbsum/1rul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rul 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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [https://pdbe.org/1rul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [https://www.ebi.ac.uk/pdbsum/1rul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rul ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GCAM_MOUSE GCAM_MOUSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 38:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Eschenmoser, A]]	+	[[Category: Eschenmoser A]]
-	[[Category: Lerner~~, R A~~]]	+	[[Category: Lerner RA]]
-	[[Category: Wentworth~~, A D~~]]	+	[[Category: Wentworth AD]]
-	[[Category: Wentworth, P]]	+	[[Category: Wentworth Jr P]]
-	[[Category: Wilson~~, I A~~]]	+	[[Category: Wilson IA]]
-	[[Category: Zhu, X]]	+	[[Category: Zhu X]]
-	~~[[Category: Amino acid modification]]~~	+
-	~~[[Category: Catalytic antibody]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin]]~~	+
-	~~[[Category: Water oxidation~~]]	+

OCA at 06:03, 28 April 2021

OCA — Wed, 28 Apr 2021 06:03:48 GMT

←Older revision		Revision as of 06:03, 28 April 2021
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	<StructureSection load='1rul' size='340' side='right'caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='1rul' size='340' side='right'caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RUL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RUL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ncw\|1ncw]], [[1nd0\|1nd0]], [[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ncw\|1ncw]], [[1nd0\|1nd0]], [[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [~~http~~://pdbe.org/1rul PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rul PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rul 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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [https://pdbe.org/1rul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [https://www.ebi.ac.uk/pdbsum/1rul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rul ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:01, 24 July 2019

OCA — Wed, 24 Jul 2019 07:01:15 GMT

←Older revision		Revision as of 07:01, 24 July 2019
Line 1:		Line 1:

	==Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.==		==Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.==
-	<StructureSection load='1rul' size='340' side='right' caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>	+	<StructureSection load='1rul' size='340' side='right'caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RUL FirstGlance]. <br>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Eschenmoser, A]]		[[Category: Eschenmoser, A]]

OCA at 07:11, 8 March 2018

OCA — Thu, 08 Mar 2018 07:11:12 GMT

←Older revision		Revision as of 07:11, 8 March 2018
Line 1:		Line 1:
		+
	==Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.==		==Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.==
	<StructureSection load='1rul' size='340' side='right' caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='1rul' size='340' side='right' caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ncw\|1ncw]], [[1nd0\|1nd0]], [[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://pdbe.org/1rul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul 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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://pdbe.org/1rul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rul ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ru/1rul_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ru/1rul_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>
	</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=1rul ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:

	==See Also==		==See Also==
-	*[[Monoclonal ~~Antibody~~\|Monoclonal ~~Antibody~~]]	+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:34, 11 September 2015

OCA — Fri, 11 Sep 2015 15:34:57 GMT

←Older revision		Revision as of 15:34, 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=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul 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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://pdbe.org/1rul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1rul" style="background-color:#fffaf0;"></div>

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

OCA at 07:26, 6 January 2015

OCA — Tue, 06 Jan 2015 07:26:23 GMT

←Older revision		Revision as of 07:26, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RUL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul 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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul 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: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Eschenmoser, A.]]	+	[[Category: Eschenmoser, A]]
-	[[Category: Lerner, R A.]]	+	[[Category: Lerner, R A]]
-	[[Category: Wentworth, A D.]]	+	[[Category: Wentworth, A D]]
-	[[Category: Wentworth, P.]]	+	[[Category: Wentworth, P]]
-	[[Category: Wilson, I A.]]	+	[[Category: Wilson, I A]]
-	[[Category: Zhu, X.]]	+	[[Category: Zhu, X]]
	[[Category: Amino acid modification]]		[[Category: Amino acid modification]]
	[[Category: Catalytic antibody]]		[[Category: Catalytic antibody]]

OCA at 04:25, 3 October 2014

OCA — Fri, 03 Oct 2014 04:25:05 GMT

←Older revision		Revision as of 04:25, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1rul\| PDB=1rul \| SCENE= }}~~	+	==Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.==
-	===Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.===	+	<StructureSection load='1rul' size='340' side='right' caption='[[1rul]], [[Resolution\|resolution]] 1.88Å' scene=''>
-	~~{{ABSTRACT_PUBMED_14982995}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rul]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RUL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ru9\|1ru9]], [[1rua\|1rua]], [[1ruk\|1ruk]], [[1rum\|1rum]], [[1rup\|1rup]]</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=1rul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rul RCSB], [http://www.ebi.ac.uk/pdbsum/1rul 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/ru/1rul_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 ==
		+	Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated. Herein, we report structural evidence for modifications of two specific antibody residues within the interfacial region of the variable and constant domains of different murine antibody antigen-binding fragments (Fabs) by reactive species generated during the antibody-catalyzed water oxidation process. Crystal structure analyses of murine Fabs 4C6 and 13G5 after UV-irradiation revealed complex oxidative modifications to tryptophan L163 and, in 4C6, hydroxylation of the Cgamma of glutamine H6. These discrete modifications of specific residues add further support for the "active site" of the water-oxidation pathway being located within the interfacial region of the constant and variable domains and highlight the general resistance of the antibody molecule to oxidation by reactive oxygen species generated during the water-oxidation process.

-	~~==About this Structure==~~	+	Probing the antibody-catalyzed water-oxidation pathway at atomic resolution.,Zhu X, Wentworth P Jr, Wentworth AD, Eschenmoser A, Lerner RA, Wilson IA Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2247-52. PMID:14982995<ref>PMID:14982995</ref>
-	~~[[1rul]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1RUL OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:014982995</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibody\|Monoclonal Antibody]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Eschenmoser, A.]]		[[Category: Eschenmoser, A.]]

OCA at 18:18, 19 June 2013

OCA — Wed, 19 Jun 2013 18:18:14 GMT

←Older revision		Revision as of 18:18, 19 June 2013
Line 1:		Line 1:
-	[[Image:1rul.png\|left\|200px]]
-
	{{STRUCTURE_1rul\| PDB=1rul \| SCENE= }}		{{STRUCTURE_1rul\| PDB=1rul \| SCENE= }}
-
	===Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.===		===Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.===
-
	{{ABSTRACT_PUBMED_14982995}}		{{ABSTRACT_PUBMED_14982995}}

Line 11:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:014982995</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014982995</ref><references group="xtra"/><references/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Eschenmoser, A.]]		[[Category: Eschenmoser, A.]]

OCA at 09:42, 16 January 2013

OCA — Wed, 16 Jan 2013 09:42:39 GMT

←Older revision		Revision as of 09:42, 16 January 2013
Line 1:		Line 1:
	[[Image:1rul.png\|left\|200px]]		[[Image:1rul.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1rul", 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_1rul\| PDB=1rul \| SCENE= }}		{{STRUCTURE_1rul\| PDB=1rul \| SCENE= }}

	===Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.===		===Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14982995}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14982995 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14982995}}		{{ABSTRACT_PUBMED_14982995}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14982995</ref><ref group="xtra">PMID:12742019~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014982995</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Eschenmoser, A.]]		[[Category: Eschenmoser, A.]]

OCA: Protected "1rul" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 22:44:02 GMT

Protected "1rul" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:44, 14 March 2011