6e3x - Revision history

OCA at 06:18, 11 October 2023

OCA — Wed, 11 Oct 2023 06:18:23 GMT

←Older revision		Revision as of 06:18, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6e3x' size='340' side='right'caption='[[6e3x]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6e3x' size='340' side='right'caption='[[6e3x]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e3x]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E3X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6E3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e3x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E3X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=DZ4:2-DEOXY-5-O~~-[~~(R)-HYDROXY{~~[~~(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL~~]~~AMINO}PHOSPHORYL~~]~~ADENOSINE'>DZ4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.65Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene>, <scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>~~[[~~Related_structure\|Related:~~]]~~</b~~></td><~~td class~~=~~"sblockDat"~~>~~[[4xk3\|4xk3]], [[4xk5\|4xk5]], [[4xk6\|4xk6]]~~</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=6e3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e3x OCA], [https://pdbe.org/6e3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e3x RCSB], [https://www.ebi.ac.uk/pdbsum/6e3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e3x ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=6e3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e3x OCA], [~~http~~://pdbe.org/6e3x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6e3x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6e3x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6e3x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>	+	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>

	==See Also==		==See Also==
Line 19:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Koag, M C]]	+	[[Category: Koag M-C]]
-	[[Category: Lee, S]]	+	[[Category: Lee S]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 10:25, 18 December 2019

OCA — Wed, 18 Dec 2019 10:25:17 GMT

←Older revision		Revision as of 10:25, 18 December 2019
Line 3:		Line 3:
	<StructureSection load='6e3x' size='340' side='right'caption='[[6e3x]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6e3x' size='340' side='right'caption='[[6e3x]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e3x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e3x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E3X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xk3\|4xk3]], [[4xk5\|4xk5]], [[4xk6\|4xk6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xk3\|4xk3]], [[4xk5\|4xk5]], [[4xk6\|4xk6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6e3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e3x OCA], [http://pdbe.org/6e3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e3x RCSB], [http://www.ebi.ac.uk/pdbsum/6e3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e3x 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=6e3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e3x OCA], [http://pdbe.org/6e3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e3x RCSB], [http://www.ebi.ac.uk/pdbsum/6e3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e3x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>		[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Koag, M C]]		[[Category: Koag, M C]]

OCA at 06:54, 3 April 2019

OCA — Wed, 03 Apr 2019 06:54:10 GMT

←Older revision		Revision as of 06:54, 3 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6e3x is ON HOLD until Paper Publication~~	+	==Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP==
-		+	<StructureSection load='6e3x' size='340' side='right'caption='[[6e3x]], [[Resolution\|resolution]] 2.65Å' scene=''>
-	~~Authors: Koag, M.-C., Lee, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6e3x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E3X FirstGlance]. <br>
-	~~Description:~~ Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene></td></tr>
-	[[Category: Koag, M.-C]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xk3\|4xk3]], [[4xk5\|4xk5]], [[4xk6\|4xk6]]</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=6e3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e3x OCA], [http://pdbe.org/6e3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e3x RCSB], [http://www.ebi.ac.uk/pdbsum/6e3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e3x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Koag, M C]]
	[[Category: Lee, S]]		[[Category: Lee, S]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 19:49, 9 August 2018

OCA — Thu, 09 Aug 2018 19:49:47 GMT

←Older revision		Revision as of 19:49, 9 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6e3x is ON HOLD	+	The entry 6e3x is ON HOLD until Paper Publication

	Authors: Koag, M.-C., Lee, S.		Authors: Koag, M.-C., Lee, S.
Line 7:		Line 7:
	Description: Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP		Description: Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lee, S]]
	[[Category: Koag, M.-C]]		[[Category: Koag, M.-C]]
		+	[[Category: Lee, S]]

OCA: Protected "6e3x" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2018 05:54:56 GMT

Protected "6e3x" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:54, 25 July 2018

OCA: New page: '''Unreleased structure''' The entry 6e3x is ON HOLD Authors: Koag, M.-C., Lee, S. Description: Structure of human DNA polymerase beta complexed with 8OA in the template base paired wi...

OCA — Wed, 25 Jul 2018 05:54:55 GMT

New page: '''Unreleased structure''' The entry 6e3x is ON HOLD Authors: Koag, M.-C., Lee, S. Description: Structure of human DNA polymerase beta complexed with 8OA in the template base paired wi...

New page

'''Unreleased structure'''

The entry 6e3x is ON HOLD

Authors: Koag, M.-C., Lee, S.

Description: Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
[[Category: Unreleased Structures]]
[[Category: Lee, S]]
[[Category: Koag, M.-C]]