3d0p - Revision history

OCA at 12:36, 30 August 2023

OCA — Wed, 30 Aug 2023 12:36:47 GMT

←Older revision		Revision as of 12:36, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3d0p' size='340' side='right'caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3d0p' size='340' side='right'caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D0P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [https://pdbe.org/3d0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [https://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p 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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [https://pdbe.org/3d0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [https://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~RNH1_BACHD RNH1_BACHD]~~] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	+	[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alkalihalobacillus halodurans C-125]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease H]]~~	+	[[Category: Egli M]]
-	[[Category: Egli, M]]	+	[[Category: Pallan PS]]
-	[[Category: Pallan~~, P S]]~~	+
-	~~[[Category: A-form]]~~	+
-	~~[[Category: B-form]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Manganese]]~~	+
-	~~[[Category: Metal ion]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Rnase h-dna complex~~]]	+

OCA at 19:17, 20 October 2021

OCA — Wed, 20 Oct 2021 19:17:28 GMT

←Older revision		Revision as of 19:17, 20 October 2021
Line 3:		Line 3:
	<StructureSection load='3d0p' size='340' side='right'caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3d0p' size='340' side='right'caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3D0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D0P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [~~http~~://pdbe.org/3d0p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p 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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [https://pdbe.org/3d0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [https://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	+	[[https://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:55, 19 August 2020

OCA — Wed, 19 Aug 2020 06:55:38 GMT

←Older revision		Revision as of 06:55, 19 August 2020
Line 1:		Line 1:

	==Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex==		==Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex==
-	<StructureSection load='3d0p' size='340' side='right' caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3d0p' size='340' side='right'caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3D0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3D0P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://pdbe.org/3d0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p 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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://pdbe.org/3d0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==
Line 37:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Egli, M]]		[[Category: Egli, M]]

OCA at 09:56, 14 November 2018

OCA — Wed, 14 Nov 2018 09:56:27 GMT

←Older revision		Revision as of 09:56, 14 November 2018
Line 1:		Line 1:
		+
	==Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex==		==Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex==
	<StructureSection load='3d0p' size='340' side='right' caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3d0p' size='340' side='right' caption='[[3d0p]], [[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=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://pdbe.org/3d0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p 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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://pdbe.org/3d0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/3d0p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/3d0p_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 41:		Line 42:
	[[Category: A-form]]		[[Category: A-form]]
	[[Category: B-form]]		[[Category: B-form]]
		+	[[Category: Cytoplasm]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:50, 9 February 2016

OCA — Tue, 09 Feb 2016 06:50:17 GMT

←Older revision		Revision as of 06:50, 9 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p 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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://pdbe.org/3d0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<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=3d0p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 3d0p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
-	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:10, 25 December 2014

OCA — Thu, 25 Dec 2014 05:10:04 GMT

←Older revision		Revision as of 05:10, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D0P FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D0P FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p 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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
		+	*[[Temp\|Temp]]
		+	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
-	[[Category: Egli, M.]]	+	[[Category: Egli, M]]
-	[[Category: Pallan, P S.]]	+	[[Category: Pallan, P S]]
	[[Category: A-form]]		[[Category: A-form]]
	[[Category: B-form]]		[[Category: B-form]]

OCA at 07:07, 29 September 2014

OCA — Mon, 29 Sep 2014 07:07:13 GMT

←Older revision		Revision as of 07:07, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:3d0p.~~png\|left~~\|200px]]	+	==Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex==
		+	<StructureSection load='3d0p' size='340' side='right' caption='[[3d0p]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D0P FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></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=3d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d0p RCSB], [http://www.ebi.ac.uk/pdbsum/3d0p 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/d0/3d0p_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 ==
		+	Ribonuclease HI (RNase H) is a member of the nucleotidyl-transferase superfamily and endo-nucleolytically cleaves the RNA portion in RNA/DNA hybrids and removes RNA primers from Okazaki fragments. The enzyme also binds RNA and DNA duplexes but is unable to cleave either. Three-dimensional structures of bacterial and human RNase H catalytic domains bound to RNA/DNA hybrids have revealed the basis for substrate recognition and the mechanism of cleavage. In order to visualize the enzyme's interactions with duplex DNA and to establish the structural differences that afford tighter binding to RNA/DNA hybrids relative to dsDNA, we have determined the crystal structure of Bacillus halodurans RNase H in complex with the B-form DNA duplex [d(CGCGAATTCGCG)](2). The structure demonstrates that the inability of the enzyme to cleave DNA is due to the deviating curvature of the DNA strand relative to the substrate RNA strand and the absence of Mg(2+) at the active site. A subset of amino acids engaged in contacts to RNA 2'-hydroxyl groups in the substrate complex instead bind to bridging or non-bridging phosphodiester oxygens in the complex with dsDNA. Qualitative comparison of the enzyme's interactions with the substrate and inhibitor duplexes is consistent with the reduced binding affinity for the latter and sheds light on determinants of RNase H binding and cleavage specificity.

-	~~{{STRUCTURE_3d0p\| PDB=3d0p \| SCENE= }}~~	+	Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex.,Pallan PS, Egli M Cell Cycle. 2008 Aug 15;7(16):2562-9. Epub 2008 Aug 18. PMID:18719385<ref>PMID:18719385</ref>

-	~~===Insights into RNA~~/~~DNA hybrid recognition and processing by RNase H from~~ the ~~crystal structure of a non-specific enzyme-dsDNA complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18719385}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3d0p]] is a 4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3D0P OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018719385<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Egli, M.]]		[[Category: Egli, M.]]

OCA at 13:01, 20 October 2012

OCA — Sat, 20 Oct 2012 13:01:12 GMT

←Older revision		Revision as of 13:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3d0p]] is a 4 chain structure ~~of [[Ribonuclease]]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA].	+	[[3d0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA].

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

OCA: Protected "3d0p" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 10:39:13 GMT

Protected "3d0p" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:39, 26 July 2012

OCA at 10:39, 26 July 2012

OCA — Thu, 26 Jul 2012 10:39:11 GMT

←Older revision		Revision as of 10:39, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3d0p.png\|left\|200px]]		[[Image:3d0p.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3d0p", 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_3d0p\| PDB=3d0p \| SCENE= }}		{{STRUCTURE_3d0p\| PDB=3d0p \| SCENE= }}

	===Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex===		===Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18719385}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18719385 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18719385}}		{{ABSTRACT_PUBMED_18719385}}

	==About this Structure==		==About this Structure==
-	~~3D0P~~ is a 4 ~~chains~~ structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA].	+	[[3d0p]] is a 4 chain structure of [[Ribonuclease]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0P OCA].
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18719385~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018719385</ref><references group="xtra"/>
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Egli, M.]]		[[Category: Egli, M.]]
Line 29:		Line 20:
	[[Category: A-form]]		[[Category: A-form]]
	[[Category: B-form]]		[[Category: B-form]]
-	[[Category: Cytoplasm]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Hydrolase/dna complex]]	+	[[Category: Hydrolase-dna complex]]
	[[Category: Magnesium]]		[[Category: Magnesium]]
	[[Category: Manganese]]		[[Category: Manganese]]
Line 40:		Line 30:
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Rnase h-dna complex]]		[[Category: Rnase h-dna complex]]
-	[[Category: X-ray crystallography]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:42:29 2009''