2f62 - Revision history

OCA at 07:43, 23 August 2023

OCA — Wed, 23 Aug 2023 07:43:43 GMT

←Older revision		Revision as of 07:43, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='2f62' size='340' side='right'caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2f62' size='340' side='right'caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Trypanosoma_(trypanozoon)_brucei~~ Trypanosoma ~~(trypanozoon)~~ brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F62 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F62 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=12M:(2~~-~~ETHYLPHENYL)METHANOL'>12M</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.5Å</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=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2a0k\|2a0k]]~~, ~~[[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">Tb05.30H13.400 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6]~~ </~~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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [https://pdbe.org/2f62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [https://www.ebi.ac.uk/pdbsum/2f62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f62 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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [https://pdbe.org/2f62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [https://www.ebi.ac.uk/pdbsum/2f62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f62 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q57VC7_TRYB2 Q57VC7_TRYB2]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nucleoside deoxyribosyltransferase]]
-	[[Category: Bosch, J]]
-	[[Category: Hol, W G.J]]
-	[[Category: Robien, M A]]
-	[[Category: Structural genomic]]
-	[[Category: Nucleoside 2-deoxyribosyltransferase]]
-	[[Category: PSI, Protein structure initiative]]
-	[[Category: Sgpp]]
-	[[Category: Transferase]]
	[[Category: Trypanosoma brucei]]		[[Category: Trypanosoma brucei]]
		+	[[Category: Bosch J]]
		+	[[Category: Hol WGJ]]
		+	[[Category: Robien MA]]

OCA at 10:38, 17 February 2021

OCA — Wed, 17 Feb 2021 10:38:38 GMT

←Older revision		Revision as of 10:38, 17 February 2021
Line 1:		Line 1:

	==Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound==		==Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound==
-	<StructureSection load='2f62' size='340' side='right' caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='2f62' size='340' side='right'caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2F62 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F62 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [~~http~~://pdbe.org/2f62 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2f62 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2f62 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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [https://pdbe.org/2f62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [https://www.ebi.ac.uk/pdbsum/2f62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f62 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Nucleoside deoxyribosyltransferase]]		[[Category: Nucleoside deoxyribosyltransferase]]
	[[Category: Bosch, J]]		[[Category: Bosch, J]]

OCA at 08:52, 14 June 2018

OCA — Thu, 14 Jun 2018 08:52:43 GMT

←Older revision		Revision as of 08:52, 14 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound==		==Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound==
	<StructureSection load='2f62' size='340' side='right' caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2f62' size='340' side='right' caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://pdbe.org/2f62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://pdbe.org/2f62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f62 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/2f62_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/2f62_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f62 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:42, 12 September 2015

OCA — Sat, 12 Sep 2015 00:42:30 GMT

←Older revision		Revision as of 00:42, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2f62' size='340' side='right' caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2f62' size='340' side='right' caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trypanosoma_brucei~~ Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F62 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F62 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma brucei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://pdbe.org/2f62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	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 2f62" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Nucleoside deoxyribosyltransferase]]		[[Category: Nucleoside deoxyribosyltransferase]]
-	[[Category: Trypanosoma brucei]]
	[[Category: Bosch, J]]		[[Category: Bosch, J]]
	[[Category: Hol, W G.J]]		[[Category: Hol, W G.J]]
Line 42:		Line 42:
	[[Category: Sgpp]]		[[Category: Sgpp]]
	[[Category: Transferase]]		[[Category: Transferase]]
		+	[[Category: Trypanosoma brucei]]

OCA at 09:07, 16 January 2015

OCA — Fri, 16 Jan 2015 09:07:25 GMT

←Older revision		Revision as of 09:07, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F62 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F62 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma brucei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma brucei])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Nucleoside deoxyribosyltransferase]]		[[Category: Nucleoside deoxyribosyltransferase]]
	[[Category: Trypanosoma brucei]]		[[Category: Trypanosoma brucei]]
-	[[Category: Bosch, J.]]	+	[[Category: Bosch, J]]
-	[[Category: Hol, W G.J.]]	+	[[Category: Hol, W G.J]]
-	[[Category: Robien, M A.]]	+	[[Category: Robien, M A]]
-	[[Category: ~~SGPP,~~ Structural ~~Genomics of Pathogenic Protozoa Consortium.~~]]	+	[[Category: Structural genomic]]
	[[Category: Nucleoside 2-deoxyribosyltransferase]]		[[Category: Nucleoside 2-deoxyribosyltransferase]]
-	[[Category: Protein structure initiative ~~ndrt]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi~~]]	+
	[[Category: Sgpp]]		[[Category: Sgpp]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics of pathogenic protozoa consortium]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Trypanosoma brucei]]

OCA at 10:47, 3 October 2014

OCA — Fri, 03 Oct 2014 10:47:58 GMT

←Older revision		Revision as of 10:47, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2f62\| PDB=2f62 \| SCENE= }}~~	+	==Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound==
-	===Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound===	+	<StructureSection load='2f62' size='340' side='right' caption='[[2f62]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17004709}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2f62]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F62 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12M:(2-ETHYLPHENYL)METHANOL'>12M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a0k\|2a0k]], [[2f2t\|2f2t]], [[2f64\|2f64]], [[2f67\|2f67]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb05.30H13.400 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma brucei])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] </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=2f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f62 RCSB], [http://www.ebi.ac.uk/pdbsum/2f62 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/f6/2f62_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 ==
		+	The 1.8 A resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SADa phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identify novel lead compounds, we exploited "fragment cocktail soaks". Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of approximately 10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.

-	~~==About this Structure==~~	+	Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.,Bosch J, Robien MA, Mehlin C, Boni E, Riechers A, Buckner FS, Van Voorhis WC, Myler PJ, Worthey EA, DeTitta G, Luft JR, Lauricella A, Gulde S, Anderson LA, Kalyuzhniy O, Neely HM, Ross J, Earnest TN, Soltis M, Schoenfeld L, Zucker F, Merritt EA, Fan E, Verlinde CL, Hol WG J Med Chem. 2006 Oct 5;49(20):5939-46. PMID:17004709<ref>PMID:17004709</ref>
-	~~[[2f62]] is a~~ 2 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trypanosoma_brucei Trypanosoma brucei]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2F62 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:017004709</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Nucleoside deoxyribosyltransferase]]		[[Category: Nucleoside deoxyribosyltransferase]]
	[[Category: Trypanosoma brucei]]		[[Category: Trypanosoma brucei]]

OCA at 08:49, 23 April 2014

OCA — Wed, 23 Apr 2014 08:49:17 GMT

←Older revision		Revision as of 08:49, 23 April 2014
Line 1:		Line 1:
-	[[Image:2f62.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_2f62", 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_2f62\| PDB=2f62 \| SCENE= }}		{{STRUCTURE_2f62\| PDB=2f62 \| SCENE= }}
-
	===Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound===		===Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17004709}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17004709 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17004709}}		{{ABSTRACT_PUBMED_17004709}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:017004709</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017004709</ref><references group="xtra"/><references/>
	[[Category: Nucleoside deoxyribosyltransferase]]		[[Category: Nucleoside deoxyribosyltransferase]]
	[[Category: Trypanosoma brucei]]		[[Category: Trypanosoma brucei]]

OCA: Protected "2f62" [edit=sysop:move=sysop]

OCA — Sat, 02 Jun 2012 09:57:01 GMT

Protected "2f62" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:57, 2 June 2012