3goc - Revision history

OCA at 07:08, 6 September 2023

2023-09-06T07:08:57Z

←Older revision		Revision as of 07:08, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3goc' size='340' side='right'caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3goc' size='340' side='right'caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Straw Straw~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GOC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis_MA-4680_=_NBRC_14893 Streptomyces avermitilis MA-4680 = NBRC 14893]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GOC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3~~-~~(2-HYDROXYETHYL)-2~~,~~2-BIS(HYDROXYMETHYL)PENTANE-~~1~~,5-DIOL'>YES</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]] 1.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">nfi ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.~~1~~.21.7 3.1.21.7]~~ </~~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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [https://pdbe.org/3goc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [https://www.ebi.ac.uk/pdbsum/3goc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3goc ProSAT], [https://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [https://pdbe.org/3goc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [https://www.ebi.ac.uk/pdbsum/3goc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3goc ProSAT], [https://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NFI_STRAW NFI_STRAW]] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA (By similarity).[HAMAP-Rule:MF_00801]	+	[https://www.uniprot.org/uniprot/NFI_STRAW NFI_STRAW] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA (By similarity).[HAMAP-Rule:MF_00801]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Deoxyribonuclease V]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Straw~~]]	+	[[Category: Streptomyces avermitilis MA-4680 = NBRC 14893]]
-	[[Category: Abashidze, M]]	+	[[Category: Abashidze M]]
-	[[Category: Acton~~, T B~~]]	+	[[Category: Acton TB]]
-	[[Category: Chen~~, C X~~]]	+	[[Category: Chen CX]]
-	[[Category: Cunningham, K]]	+	[[Category: Cunningham K]]
-	[[Category: Everett~~, J K~~]]	+	[[Category: Everett JK]]
-	[[Category: Fang, F]]	+	[[Category: Fang F]]
-	[[Category: Forouhar, F]]	+	[[Category: Forouhar F]]
-	[[Category: Hunt~~, J F~~]]	+	[[Category: Hunt JF]]
-	[[Category: Hussain, M]]	+	[[Category: Hussain M]]
-	[[Category: Ma, L]]	+	[[Category: Ma L]]
-	[[Category: Montelione~~, G T]]~~	+	[[Category: Montelione GT]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Nair R]]
-	[[Category: Nair, R]]	+	[[Category: Owens L]]
-	[[Category: Owens, L]]	+	[[Category: Rost B]]
-	[[Category: Rost, B]]	+	[[Category: Seetharaman J]]
-	[[Category: Seetharaman, J]]	+	[[Category: Tong L]]
-	[[Category: Tong, L]]	+	[[Category: Xiao R]]
-	[[Category: Xiao, R]]	+
-	~~[[Category: Alpha-beta protein]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Nesg]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: PSI, Protein structure initiative~~]]	+

OCA at 07:50, 16 March 2022

2022-03-16T07:50:41Z

OCA at 08:14, 24 July 2019

2019-07-24T08:14:30Z

←Older revision		Revision as of 08:14, 24 July 2019
Line 1:		Line 1:

	==Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196==		==Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196==
-	<StructureSection load='3goc' size='340' side='right' caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3goc' size='340' side='right'caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Straw Straw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Straw Straw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>
Line 24:		Line 24:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Deoxyribonuclease V]]		[[Category: Deoxyribonuclease V]]
		+	[[Category: Large Structures]]
	[[Category: Straw]]		[[Category: Straw]]
	[[Category: Abashidze, M]]		[[Category: Abashidze, M]]

OCA at 05:38, 7 December 2018

2018-12-07T05:38:34Z

←Older revision		Revision as of 05:38, 7 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196==		==Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196==
	<StructureSection load='3goc' size='340' side='right' caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3goc' size='340' side='right' caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://pdbe.org/3goc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://pdbe.org/3goc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3goc ProSAT], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/go/3goc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/go/3goc_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 02:44, 8 February 2016

2016-02-08T02:44:57Z

←Older revision		Revision as of 02:44, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3goc' size='340' side='right' caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3goc' size='340' side='right' caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_avermitilis Streptomyces avermitilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Straw Straw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~33903 Streptomyces avermitilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://pdbe.org/3goc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		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=3goc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>

Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Deoxyribonuclease V]]		[[Category: Deoxyribonuclease V]]
-	[[Category: ~~Streptomyces avermitilis~~]]	+	[[Category: Straw]]
	[[Category: Abashidze, M]]		[[Category: Abashidze, M]]
	[[Category: Acton, T B]]		[[Category: Acton, T B]]

OCA at 20:00, 24 December 2014

2014-12-24T20:00:31Z

←Older revision		Revision as of 20:00, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NFI_STRAW NFI_STRAW]] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA (By similarity).[HAMAP-Rule:MF_00801]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	[[Category: Deoxyribonuclease V]]		[[Category: Deoxyribonuclease V]]
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]
-	[[Category: Abashidze, M.]]	+	[[Category: Abashidze, M]]
-	[[Category: Acton, T B.]]	+	[[Category: Acton, T B]]
-	[[Category: Chen, C X.]]	+	[[Category: Chen, C X]]
-	[[Category: Cunningham, K.]]	+	[[Category: Cunningham, K]]
-	[[Category: Everett, J K.]]	+	[[Category: Everett, J K]]
-	[[Category: Fang, F.]]	+	[[Category: Fang, F]]
-	[[Category: Forouhar, F.]]	+	[[Category: Forouhar, F]]
-	[[Category: Hunt, J F.]]	+	[[Category: Hunt, J F]]
-	[[Category: Hussain, M.]]	+	[[Category: Hussain, M]]
-	[[Category: Ma, L.]]	+	[[Category: Ma, L]]
-	[[Category: Montelione, G T.]]	+	[[Category: Montelione, G T]]
-	[[Category: ~~NESG, Northeast~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Nair, R.]]	+	[[Category: Nair, R]]
-	[[Category: Owens, L.]]	+	[[Category: Owens, L]]
-	[[Category: Rost, B.]]	+	[[Category: Rost, B]]
-	[[Category: Seetharaman, J.]]	+	[[Category: Seetharaman, J]]
-	[[Category: Tong, L.]]	+	[[Category: Tong, L]]
-	[[Category: Xiao, R.]]	+	[[Category: Xiao, R]]
	[[Category: Alpha-beta protein]]		[[Category: Alpha-beta protein]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
Line 51:		Line 53:
	[[Category: Magnesium]]		[[Category: Magnesium]]
	[[Category: Nesg]]		[[Category: Nesg]]
-	[[Category: Northeast structural genomics consortium]]
	[[Category: Nuclease]]		[[Category: Nuclease]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi-2]]~~	+
-	~~[[Category: Structural genomic~~]]	+

OCA at 11:06, 29 September 2014

2014-09-29T11:06:38Z

←Older revision		Revision as of 11:06, 29 September 2014
Line 1:		Line 1:
-	~~[[Image:3goc.png\|left\|200px]]~~	+	==Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196==
-		+	<StructureSection load='3goc' size='340' side='right' caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{STRUCTURE_3goc\| PDB=3goc \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOC FirstGlance]. <br>
-	===Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196===	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>
-	==~~About this Structure~~==	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>
-	[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA].	+	<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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [http://www.ebi.ac.uk/pdbsum/3goc PDBsum], [http://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</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/go/3goc_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>

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
		+	__TOC__
		+	</StructureSection>
	[[Category: Deoxyribonuclease V]]		[[Category: Deoxyribonuclease V]]
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]

OCA at 08:38, 20 October 2012

2012-10-20T08:38:14Z

←Older revision		Revision as of 08:38, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3goc]] is a 2 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA].	+	[[3goc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA].

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

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

2012-07-25T20:15:38Z

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

←Older revision

Revision as of 20:15, 25 July 2012

OCA at 20:15, 25 July 2012

2012-07-25T20:15:34Z

←Older revision		Revision as of 20:15, 25 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3goc.png\|left\|200px]]

-	~~The entry~~ 3goc ~~is ON HOLD~~	+	{{STRUCTURE_3goc\| PDB=3goc \| SCENE= }}

-	~~Authors: Forouhar, F~~., Abashidze, M., Hussain, M., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Owens, L., Chen, C.X., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium	+	===Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196===

-	Description: Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Thu Apr 9 12~~:17:~~43 2009''~~	+	==About this Structure==
		+	[[3goc]] is a 2 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
		+	[[Category: Deoxyribonuclease V]]
		+	[[Category: Streptomyces avermitilis]]
		+	[[Category: Abashidze, M.]]
		+	[[Category: Acton, T B.]]
		+	[[Category: Chen, C X.]]
		+	[[Category: Cunningham, K.]]
		+	[[Category: Everett, J K.]]
		+	[[Category: Fang, F.]]
		+	[[Category: Forouhar, F.]]
		+	[[Category: Hunt, J F.]]
		+	[[Category: Hussain, M.]]
		+	[[Category: Ma, L.]]
		+	[[Category: Montelione, G T.]]
		+	[[Category: NESG, Northeast Structural Genomics Consortium.]]
		+	[[Category: Nair, R.]]
		+	[[Category: Owens, L.]]
		+	[[Category: Rost, B.]]
		+	[[Category: Seetharaman, J.]]
		+	[[Category: Tong, L.]]
		+	[[Category: Xiao, R.]]
		+	[[Category: Alpha-beta protein]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna repair]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Magnesium]]
		+	[[Category: Nesg]]
		+	[[Category: Northeast structural genomics consortium]]
		+	[[Category: Nuclease]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-2]]
		+	[[Category: Structural genomic]]

←Older revision		Revision as of 07:50, 16 March 2022
Line 3:		Line 3:
	<StructureSection load='3goc' size='340' side='right'caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3goc' size='340' side='right'caption='[[3goc]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Straw Straw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GOC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3goc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Straw Straw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GOC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YES:3-(2-HYDROXYETHYL)-2,2-BIS(HYDROXYMETHYL)PENTANE-1,5-DIOL'>YES</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [~~http~~://pdbe.org/3goc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3goc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3goc ProSAT], [~~http~~://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</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=3goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3goc OCA], [https://pdbe.org/3goc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3goc RCSB], [https://www.ebi.ac.uk/pdbsum/3goc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3goc ProSAT], [https://www.topsan.org/Proteins/NESGC/3goc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NFI_STRAW NFI_STRAW]] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA (By similarity).[HAMAP-Rule:MF_00801]	+	[[https://www.uniprot.org/uniprot/NFI_STRAW NFI_STRAW]] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA (By similarity).[HAMAP-Rule:MF_00801]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]