3kd1 - Revision history

OCA at 06:34, 19 July 2023

2023-07-19T06:34:33Z

←Older revision		Revision as of 06:34, 19 July 2023
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	<StructureSection load='3kd1' size='340' side='right'caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>		<StructureSection load='3kd1' size='340' side='right'caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpr69 Bpr69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.66Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;'>[[3kd5\|3kd5]]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43~~, ~~RB69 gp43 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])~~<~~/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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [https://pdbe.org/3kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [https://pdbe.org/3kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.	+	[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 3kd1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3kd1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpr69]]~~	+	[[Category: Escherichia phage RB69]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doublie, S]]	+	[[Category: Doublie S]]
-	[[Category: Zahn~~, K E]]~~	+	[[Category: Zahn KE]]
-	~~[[Category: Acyclic guanosine]]~~	+
-	~~[[Category: Acyclovir]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Foscarnet]]~~	+
-	~~[[Category: Foscavir]]~~	+
-	~~[[Category: Gp43]]~~	+
-	~~[[Category: Hcmv]]~~	+
-	~~[[Category: Human cytomegalovirus]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Phosphonoformic acid]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 12:23, 13 October 2021

2021-10-13T12:23:38Z

←Older revision		Revision as of 12:23, 13 October 2021
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	<StructureSection load='3kd1' size='340' side='right'caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>		<StructureSection load='3kd1' size='340' side='right'caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3kd5\|3kd5]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [~~http~~://pdbe.org/3kd1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [https://pdbe.org/3kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.	+	[[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 3kd1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3kd1" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:07, 17 July 2019

2019-07-17T11:07:36Z

←Older revision		Revision as of 11:07, 17 July 2019
Line 1:		Line 1:

	==Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.==		==Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.==
-	<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>	+	<StructureSection load='3kd1' size='340' side='right'caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
Line 24:		Line 24:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 31:
	[[Category: Bpr69]]		[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
	[[Category: Zahn, K E]]		[[Category: Zahn, K E]]

OCA at 09:03, 26 December 2018

2018-12-26T09:03:01Z

←Older revision		Revision as of 09:03, 26 December 2018
Line 3:		Line 3:
	<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>		<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://pdbe.org/3kd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 ProSAT]</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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://pdbe.org/3kd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 ProSAT]</span></td></tr>
Line 28:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]

OCA at 07:28, 18 January 2017

2017-01-18T07:28:35Z

←Older revision		Revision as of 07:28, 18 January 2017
Line 1:		Line 1:
		+
	==Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.==		==Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.==
	<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>		<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://pdbe.org/3kd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kd1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	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 3kd1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]

OCA at 06:37, 15 April 2015

2015-04-15T06:37:36Z

←Older revision		Revision as of 06:37, 15 April 2015
Line 2:		Line 2:
	<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>		<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_rb69 Enterobacteria phage rb69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 ~~Enterobacteria phage RB69~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 PDBsum]</span></td></tr>
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.		[[http://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphonoformic acid (PFA, foscarnet) belongs to a class of antiviral drugs that inhibit the human cytomegalovirus DNA polymerase (UL54) by mimicking the pyrophosphate leaving group of the nucleotide transfer reaction. Difficulties expressing UL54 have hampered investigation of the precise structural requirements rendering inhibition by this drug. However, a previously engineered chimeric DNA polymerase, constructed by mutating the homologous polymerase from bacteriophage RB69 (gp43) to express several variable elements from UL54, can bypass this obstacle because of its favorable expression and acquired sensitivity to PFA (Tchesnokov, E. P., Obikhod, A., Schinazi, R. F., and Gotte, M. (2008) J. Biol. Chem. 283, 34218-34228). Here, we compare two crystal structures that depict the chimeric DNA polymerase with and without PFA bound. PFA is visualized for the first time in the active site of a DNA polymerase, where interactions are resolved between the PP(i) mimic and two basic residues absolutely conserved in the fingers domain of family B polymerases. PFA also chelates metal ion B, the cation that contacts the triphosphate tail of the incoming nucleotide. These DNA complexes utilize a primer-template pair enzymatically chain-terminated by incorporation of acyclo-GMP, the phosphorylated form of the anti-herpes drug acyclovir. We postulate that the V478W mutation present in the chimera is critical in that it pushes the fingers domain to more readily adopt the closed conformation whether or not the drug is bound. The closed state of the fingers domain traps the variant polymerase in the untranslocated state and increases affinity for PFA. This finding provides a model for the mechanism of UL54 stalling by PFA.
		+
		+	Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase.,Zahn KE, Tchesnokov EP, Gotte M, Doublie S J Biol Chem. 2011 Jul 15;286(28):25246-55. doi: 10.1074/jbc.M111.248864. Epub, 2011 May 12. PMID:21566148<ref>PMID:21566148</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Enterobacteria phage rb69]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
	[[Category: Zahn, K E]]		[[Category: Zahn, K E]]

OCA at 13:45, 25 December 2014

2014-12-25T13:45:03Z

←Older revision		Revision as of 13:45, 25 December 2014
Line 10:		Line 10:
	<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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.

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

OCA at 08:46, 9 December 2014

2014-12-09T08:46:44Z

←Older revision		Revision as of 08:46, 9 December 2014
Line 1:		Line 1:
-	~~[[Image:3kd1.png\|left\|200px]]~~	+	==Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.==
-		+	<StructureSection load='3kd1' size='340' side='right' caption='[[3kd1]], [[Resolution\|resolution]] 2.66Å' scene=''>
-	~~{{STRUCTURE_3kd1\| PDB=3kd1 \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KD1 FirstGlance]. <br>
-	===Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.===	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4DG:2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>4DG</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kd5\|3kd5]]</td></tr>
-	==~~About this Structure~~==	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, RB69 gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])</td></tr>
-	[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA].	+	<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=3kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kd1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kd1 RCSB], [http://www.ebi.ac.uk/pdbsum/3kd1 PDBsum]</span></td></tr>
		+	</table>

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
		+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]
-	[[Category: Doublie, S.]]	+	[[Category: Doublie, S]]
-	[[Category: Zahn, K E.]]	+	[[Category: Zahn, K E]]
	[[Category: Acyclic guanosine]]		[[Category: Acyclic guanosine]]
	[[Category: Acyclovir]]		[[Category: Acyclovir]]

OCA at 17:24, 20 October 2012

2012-10-20T17:24:27Z

←Older revision		Revision as of 17:24, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3kd1]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA].	+	[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA].

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

OCA at 00:47, 27 July 2012

2012-07-27T00:47:44Z

←Older revision		Revision as of 00:47, 27 July 2012
Line 1:		Line 1:
-	[[Image:3kd1.~~jpg~~\|left\|200px]]	+	[[Image:3kd1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kd1", 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.
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	{{STRUCTURE_3kd1\| PDB=3kd1 \| SCENE= }}		{{STRUCTURE_3kd1\| PDB=3kd1 \| SCENE= }}

Line 13:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3kd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA].	+	[[3kd1]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KD1 OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]
	[[Category: Doublie, S.]]		[[Category: Doublie, S.]]
	[[Category: Zahn, K E.]]		[[Category: Zahn, K E.]]
		+	[[Category: Acyclic guanosine]]
		+	[[Category: Acyclovir]]
		+	[[Category: Dna replication]]
		+	[[Category: Dna-binding]]
		+	[[Category: Dna-directed dna polymerase]]
		+	[[Category: Exonuclease]]
		+	[[Category: Foscarnet]]
		+	[[Category: Foscavir]]
		+	[[Category: Gp43]]
		+	[[Category: Hcmv]]
		+	[[Category: Human cytomegalovirus]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Phosphonoformic acid]]
		+	[[Category: Polymerase]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-dna complex]]