3d1g - Revision history

OCA at 12:37, 30 August 2023

2023-08-30T12:37:19Z

←Older revision		Revision as of 12:37, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3d1g' size='340' side='right'caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='3d1g' size='340' side='right'caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=322:[(5R)~~-~~5-(2~~,~~3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</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]] 1.64Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2pol\|2pol]], [[3bep\|3bep]], [[3d1e\|3d1e]], [[3d1f\|3d1f]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dnaN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562 Escherichia coli])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~https://en.wikipedia.org/wiki/DNA~~-~~directed_DNA_polymerase DNA~~-~~directed DNA polymerase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~2~~.7.7.7 2.7.7.7~~] </~~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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [https://pdbe.org/3d1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [https://www.ebi.ac.uk/pdbsum/3d1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1g 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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [https://pdbe.org/3d1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [https://www.ebi.ac.uk/pdbsum/3d1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.	+	[https://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 3d1g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3d1g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: DNA-directed DNA polymerase]]~~	+	[[Category: Escherichia coli K-12]]
-	[[Category: Escherichia coli]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Donnell, M O]]~~	+	[[Category: Georgescu RE]]
-	[[Category: Georgescu~~, R E~~]]	+	[[Category: Kong X-P]]
-	[[Category: Kong, X P]]	+	[[Category: Kuriyan J]]
-	[[Category: Kuriyan, J]]	+	[[Category: O'Donnell M]]
-	[[Category: ~~Seung-Sup, K]]~~	+	[[Category: Seung-Sup K]]
-	~~[[Category: Yurieva,~~ O]]	+	[[Category: Yurieva O]]
-	[[Category: ~~Antibiotic target~~]]	+
-	[[Category: ~~Chemical probe]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna sliding clamp]]~~	+
-	~~[[Category: Rational drug design]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:50, 2 February 2022

2022-02-02T07:50:45Z

←Older revision		Revision as of 07:50, 2 February 2022
Line 1:		Line 1:

	==Structure of a small molecule inhibitor bound to a DNA sliding clamp==		==Structure of a small molecule inhibitor bound to a DNA sliding clamp==
-	<StructureSection load='3d1g' size='340' side='right' caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='3d1g' size='340' side='right'caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3D1G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pol\|2pol]], [[3bep\|3bep]], [[3d1e\|3d1e]], [[3d1f\|3d1f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pol\|2pol]], [[3bep\|3bep]], [[3d1e\|3d1e]], [[3d1f\|3d1f]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [~~http~~://pdbe.org/3d1g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3d1g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1g 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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [https://pdbe.org/3d1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [https://www.ebi.ac.uk/pdbsum/3d1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.	+	[[https://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Donnell, M O]]		[[Category: Donnell, M O]]
	[[Category: Georgescu, R E]]		[[Category: Georgescu, R E]]

OCA at 19:13, 24 January 2018

2018-01-24T19:13:38Z

←Older revision		Revision as of 19:13, 24 January 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1g_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1g_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 39:		Line 39:
	[[Category: Donnell, M O]]		[[Category: Donnell, M O]]
	[[Category: Georgescu, R E]]		[[Category: Georgescu, R E]]
-	[[Category: Kong, X-P]]	+	[[Category: Kong, X P]]
	[[Category: Kuriyan, J]]		[[Category: Kuriyan, J]]
	[[Category: Seung-Sup, K]]		[[Category: Seung-Sup, K]]

OCA at 08:40, 25 October 2017

2017-10-25T08:40:37Z

←Older revision		Revision as of 08:40, 25 October 2017
Line 1:		Line 1:
		+
	==Structure of a small molecule inhibitor bound to a DNA sliding clamp==		==Structure of a small molecule inhibitor bound to a DNA sliding clamp==
	<StructureSection load='3d1g' size='340' side='right' caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='3d1g' size='340' side='right' caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://pdbe.org/3d1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g 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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://pdbe.org/3d1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 3d1g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3d1g" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:22, 8 February 2016

2016-02-08T14:22:29Z

←Older revision		Revision as of 14:22, 8 February 2016
Line 7:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g 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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://pdbe.org/3d1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g PDBsum]</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=3d1g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3d1g" style="background-color:#fffaf0;"></div>

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

OCA at 23:58, 24 December 2014

2014-12-24T23:58:28Z

←Older revision		Revision as of 23:58, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D1G FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D1G FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pol\|2pol]], [[3bep\|3bep]], [[3d1e\|3d1e]], [[3d1f\|3d1f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pol\|2pol]], [[3bep\|3bep]], [[3d1e\|3d1e]], [[3d1f\|3d1f]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g 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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Donnell, M O.]]	+	[[Category: Donnell, M O]]
-	[[Category: Georgescu, R E.]]	+	[[Category: Georgescu, R E]]
-	[[Category: Kong, X-P.]]	+	[[Category: Kong, X-P]]
-	[[Category: Kuriyan, J.]]	+	[[Category: Kuriyan, J]]
-	[[Category: Seung-Sup, K.]]	+	[[Category: Seung-Sup, K]]
-	[[Category: Yurieva, O.]]	+	[[Category: Yurieva, O]]
	[[Category: Antibiotic target]]		[[Category: Antibiotic target]]
	[[Category: Chemical probe]]		[[Category: Chemical probe]]

OCA at 09:35, 29 September 2014

2014-09-29T09:35:42Z

←Older revision		Revision as of 09:35, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3d1g.~~png~~\|~~left~~\|200px]]	+	==Structure of a small molecule inhibitor bound to a DNA sliding clamp==
		+	<StructureSection load='3d1g' size='340' side='right' caption='[[3d1g]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3d1g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D1G FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pol\|2pol]], [[3bep\|3bep]], [[3d1e\|3d1e]], [[3d1f\|3d1f]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [http://www.ebi.ac.uk/pdbsum/3d1g 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/d1/3d1g_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 ==
		+	DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA polymerases II, III, and IV. To understand the molecular basis of this discrimination, the cocrystal structure of the chemical inhibitor is solved in complex with beta and is compared with the structures of Pol II, Pol III, and Pol IV peptides bound to beta. The analysis reveals that the small molecule localizes in a region of the clamp to which the DNA polymerases attach in different ways. The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target.

-	~~{{STRUCTURE_3d1g\| PDB=3d1g \| SCENE= }}~~	+	Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.,Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, O'Donnell M Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11116-21. Epub 2008 Aug 4. PMID:18678908<ref>PMID:18678908</ref>

-	~~===Structure~~ of ~~a small molecule inhibitor bound to a DNA sliding clamp===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18678908}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3d1g]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018678908<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 10:26, 20 October 2012

2012-10-20T10:26:47Z

←Older revision		Revision as of 10:26, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3d1g]] is a 2 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA].	+	[[3d1g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA].

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

OCA: Protected "3d1g" [edit=sysop:move=sysop]

2012-07-26T02:09:08Z

Protected "3d1g" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:09, 26 July 2012

OCA at 02:09, 26 July 2012

2012-07-26T02:09:07Z

←Older revision		Revision as of 02:09, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3d1g.png\|left\|200px]]		[[Image:3d1g.png\|left\|200px]]

-	<!--
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-	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),
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	{{STRUCTURE_3d1g\| PDB=3d1g \| SCENE= }}		{{STRUCTURE_3d1g\| PDB=3d1g \| SCENE= }}

	===Structure of a small molecule inhibitor bound to a DNA sliding clamp===		===Structure of a small molecule inhibitor bound to a DNA sliding clamp===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18678908}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18678908 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18678908}}		{{ABSTRACT_PUBMED_18678908}}

	==About this Structure==		==About this Structure==
-	~~3D1G~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA].	+	[[3d1g]] is a 2 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18678908~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018678908</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 40:		Line 31:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:36:28 2009''