3hiw - Revision history

OCA at 10:00, 21 February 2024

OCA — Wed, 21 Feb 2024 10:00:23 GMT

←Older revision		Revision as of 10:00, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3hiw' size='340' side='right'caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3hiw' size='340' side='right'caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Common_soapwort Common soapwort~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HIW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</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]] 1.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [https://pdbe.org/3hiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [https://www.ebi.ac.uk/pdbsum/3hiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiw 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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [https://pdbe.org/3hiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [https://www.ebi.ac.uk/pdbsum/3hiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2QEH4_SAPOF Q2QEH4_SAPOF]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3hiw 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=3hiw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple pi-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the pi-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H(2)O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.
-
-	Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.,Ho MC, Sturm MB, Almo SC, Schramm VL Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20276-81. Epub 2009 Nov 17. PMID:19920175<ref>PMID:19920175</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3hiw" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Common soapwort]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Saponaria officinalis]]
-	[[Category: ~~Ho, M~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~Schramm, V L]]~~	+	[[Category: Ho M]]
-	~~[[Category: Sturm,~~ M B]]	+	[[Category: Schramm VL]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Sturm MB]]
-	[[Category: ~~Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Plant defense]]~~	+
-	~~[[Category: Protein synthesis inhibitor]]~~	+
-	~~[[Category: Ribosome inactivating protein]]~~	+
-	~~[[Category: Rip]]~~	+
-	~~[[Category: Toxin]]~~	+
-	~~[[Category: Transition state~~]]	+

OCA at 12:49, 23 March 2022

OCA — Wed, 23 Mar 2022 12:49:17 GMT

←Older revision		Revision as of 12:49, 23 March 2022
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	<StructureSection load='3hiw' size='340' side='right'caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3hiw' size='340' side='right'caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Common_soapwort Common soapwort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Common_soapwort Common soapwort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HIW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [~~http~~://pdbe.org/3hiw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hiw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiw 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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [https://pdbe.org/3hiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [https://www.ebi.ac.uk/pdbsum/3hiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiw ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:12, 7 August 2019

OCA — Wed, 07 Aug 2019 07:12:18 GMT

←Older revision		Revision as of 07:12, 7 August 2019
Line 1:		Line 1:

	==Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue==		==Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue==
-	<StructureSection load='3hiw' size='340' side='right' caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3hiw' size='340' side='right'caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_soapwort Common soapwort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HIW FirstGlance]. <br>		<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_soapwort Common soapwort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HIW FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hi/3hiw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hi/3hiw_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 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Common soapwort]]		[[Category: Common soapwort]]
		+	[[Category: Large Structures]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Ho, M]]		[[Category: Ho, M]]

OCA at 07:38, 1 November 2017

OCA — Wed, 01 Nov 2017 07:38:20 GMT

←Older revision		Revision as of 07:38, 1 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue==		==Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue==
	<StructureSection load='3hiw' size='340' side='right' caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3hiw' size='340' side='right' caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [http://pdbe.org/3hiw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [http://www.ebi.ac.uk/pdbsum/3hiw 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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [http://pdbe.org/3hiw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [http://www.ebi.ac.uk/pdbsum/3hiw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiw ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 06:43, 9 February 2016

OCA — Tue, 09 Feb 2016 06:43:21 GMT

←Older revision		Revision as of 06:43, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3hiw' size='340' side='right' caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3hiw' size='340' side='right' caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saponaria_officinalis Saponaria officinalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_soapwort Common soapwort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HIW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [http://www.ebi.ac.uk/pdbsum/3hiw 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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [http://pdbe.org/3hiw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [http://www.ebi.ac.uk/pdbsum/3hiw PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<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=3hiw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	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 3hiw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saponaria officinalis~~]]	+	[[Category: Common soapwort]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Ho, M]]		[[Category: Ho, M]]

OCA at 13:26, 6 November 2014

OCA — Thu, 06 Nov 2014 13:26:43 GMT

←Older revision		Revision as of 13:26, 6 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3hiw.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue==
		+	<StructureSection load='3hiw' size='340' side='right' caption='[[3hiw]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hiw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HIW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2X:9,9-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F 3,2-L 3,2-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)'>C2X</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hio\|3hio]], [[3hiq\|3hiq]], [[3his\|3his]], [[3hit\|3hit]], [[3hiv\|3hiv]]</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=3hiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hiw RCSB], [http://www.ebi.ac.uk/pdbsum/3hiw 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/hi/3hiw_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 ==
		+	Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple pi-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the pi-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H(2)O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.

-	~~{{STRUCTURE_3hiw\| PDB=3hiw \| SCENE= }}~~	+	Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.,Ho MC, Sturm MB, Almo SC, Schramm VL Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20276-81. Epub 2009 Nov 17. PMID:19920175<ref>PMID:19920175</ref>

-	~~===Crystal structure~~ of ~~Saporin-L1 in complex with~~ the ~~cyclic tetranucleotide inhibitor, a transition state analogue===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19920175}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3hiw]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saponaria_officinalis Saponaria officinalis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019920175<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saponaria officinalis]]		[[Category: Saponaria officinalis]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Ho, M.]]	+	[[Category: Ho, M]]
-	[[Category: Schramm, V L.]]	+	[[Category: Schramm, V L]]
-	[[Category: Sturm, M B.]]	+	[[Category: Sturm, M B]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

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

OCA — Wed, 06 Mar 2013 14:53:52 GMT

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

←Older revision

Revision as of 14:53, 6 March 2013

OCA at 14:53, 6 March 2013

OCA — Wed, 06 Mar 2013 14:53:50 GMT

←Older revision		Revision as of 14:53, 6 March 2013
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-	{{Seed}}
	[[Image:3hiw.png\|left\|200px]]		[[Image:3hiw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3hiw", 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_3hiw\| PDB=3hiw \| SCENE= }}		{{STRUCTURE_3hiw\| PDB=3hiw \| SCENE= }}

	===Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue===		===Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19920175}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19920175 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19920175}}		{{ABSTRACT_PUBMED_19920175}}

	==About this Structure==		==About this Structure==
-	~~3HIW~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA].	+	[[3hiw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19920175~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019920175</ref><references group="xtra"/>
	[[Category: Saponaria officinalis]]		[[Category: Saponaria officinalis]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
Line 37:		Line 25:
	[[Category: Toxin]]		[[Category: Toxin]]
	[[Category: Transition state]]		[[Category: Transition state]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 08:47:56 2010''

OCA at 05:47, 21 April 2010

OCA — Wed, 21 Apr 2010 05:47:58 GMT

←Older revision		Revision as of 05:47, 21 April 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3HIW is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA].	+	3HIW is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIW OCA].

	==Reference==		==Reference==
Line 30:		Line 30:
	[[Category: Sturm, M B.]]		[[Category: Sturm, M B.]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Hydrolase/hydrolase inhibitor complex]]	+	[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Plant defense]]		[[Category: Plant defense]]
	[[Category: Protein synthesis inhibitor]]		[[Category: Protein synthesis inhibitor]]
Line 38:		Line 38:
	[[Category: Transition state]]		[[Category: Transition state]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 16 11~~:28:~~41 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 08:47:56 2010''

OCA at 09:28, 16 December 2009

OCA — Wed, 16 Dec 2009 09:28:42 GMT

←Older revision		Revision as of 09:28, 16 December 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3hiw.~~jpg~~\|left\|200px]]	+	[[Image:3hiw.png\|left\|200px]]

	<!--		<!--
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	[[Category: Transition state]]		[[Category: Transition state]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec ~~9 14~~:56:43 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 11:28:41 2009''