5dai - Revision history

OCA at 08:44, 27 September 2023

2023-09-27T08:44:49Z

←Older revision		Revision as of 08:44, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DAI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [https://pdbe.org/5dai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [https://www.ebi.ac.uk/pdbsum/5dai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai 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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [https://pdbe.org/5dai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [https://www.ebi.ac.uk/pdbsum/5dai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:28, 21 June 2023

2023-06-21T10:28:26Z

←Older revision		Revision as of 10:28, 21 June 2023
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	<StructureSection load='5dai' size='340' side='right'caption='[[5dai]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5dai' size='340' side='right'caption='[[5dai]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DAI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lx1\|3lx1]], [[5da7\|5da7]]</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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [https://pdbe.org/5dai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [https://www.ebi.ac.uk/pdbsum/5dai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcn1, TK0535 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [~~http~~://pdbe.org/5dai PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dai PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PCNA1_THEKO PCNA1_THEKO]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.[HAMAP-Rule:MF_00317]	+	[https://www.uniprot.org/uniprot/PCNA1_THEKO PCNA1_THEKO] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.[HAMAP-Rule:MF_00317]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	*[[Proliferating cell nuclear antigen 3D structures\|Proliferating cell nuclear antigen 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Altieri, A S~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: ~~Kelman, Z~~]]	+	[[Category: Altieri AS]]
-	[[Category: ~~Ladner, J E~~]]	+	[[Category: Kelman Z]]
-	[[Category: ~~Complex]]~~	+	[[Category: Ladner JE]]
-	~~[[Category: Pip box binder]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:57, 8 April 2020

2020-04-08T07:57:22Z

←Older revision		Revision as of 07:57, 8 April 2020
Line 1:		Line 1:

	==Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide==		==Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide==
-	<StructureSection load='5dai' size='340' side='right' caption='[[5dai]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5dai' size='340' side='right'caption='[[5dai]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lx1\|3lx1]], [[5da7\|5da7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lx1\|3lx1]], [[5da7\|5da7]]</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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [http://pdbe.org/5dai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [http://www.ebi.ac.uk/pdbsum/5dai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcn1, TK0535 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [http://pdbe.org/5dai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [http://www.ebi.ac.uk/pdbsum/5dai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5dai" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dai" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Altieri, A S]]		[[Category: Altieri, A S]]
	[[Category: Kelman, Z]]		[[Category: Kelman, Z]]

OCA at 08:14, 10 August 2016

2016-08-10T08:14:21Z

←Older revision		Revision as of 08:14, 10 August 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lx1\|3lx1]], [[5da7\|5da7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lx1\|3lx1]], [[5da7\|5da7]]</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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [http://pdbe.org/5dai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [http://www.ebi.ac.uk/pdbsum/5dai 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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [http://pdbe.org/5dai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [http://www.ebi.ac.uk/pdbsum/5dai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dai ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:59, 1 June 2016

2016-06-01T07:59:26Z

←Older revision		Revision as of 07:59, 1 June 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PCNA1_THEKO PCNA1_THEKO]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.[HAMAP-Rule:MF_00317]		[[http://www.uniprot.org/uniprot/PCNA1_THEKO PCNA1_THEKO]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.[HAMAP-Rule:MF_00317]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.
		+
		+	A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp.,Altieri AS, Ladner JE, Li Z, Robinson H, Sallman ZF, Marino JP, Kelman Z Nucleic Acids Res. 2016 May 3. pii: gkw351. PMID:27141962<ref>PMID:27141962</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dai" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:05, 15 May 2016

2016-05-15T17:05:29Z

←Older revision		Revision as of 17:05, 15 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dai is ~~ON HOLD until Paper Publication~~	+	==Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide==
-		+	<StructureSection load='5dai' size='340' side='right' caption='[[5dai]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Ladner~~, J.E., ~~Altieri, A~~.S., ~~Kelman~~, Z.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dai]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DAI FirstGlance]. <br>
-	~~Description~~: ~~PCNA bound~~ to ~~FEN~~-~~1 peptide~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lx1\|3lx1]], [[5da7\|5da7]]</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=5dai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dai OCA], [http://pdbe.org/5dai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dai RCSB], [http://www.ebi.ac.uk/pdbsum/5dai PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCNA1_THEKO PCNA1_THEKO]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.[HAMAP-Rule:MF_00317]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Altieri, A S]]
	[[Category: Kelman, Z]]		[[Category: Kelman, Z]]
-	[[Category: ~~Altieri~~, ~~A.S~~]]	+	[[Category: Ladner, J E]]
-	[[Category: ~~Ladner, J.E~~]]	+	[[Category: Complex]]
		+	[[Category: Pip box binder]]
		+	[[Category: Transferase]]

OCA at 11:22, 2 September 2015

2015-09-02T11:22:42Z

←Older revision		Revision as of 11:22, 2 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dai is ON HOLD	+	The entry 5dai is ON HOLD until Paper Publication

	Authors: Ladner, J.E., Altieri, A.S., Kelman, Z.		Authors: Ladner, J.E., Altieri, A.S., Kelman, Z.

OCA: Protected "5dai" [edit=sysop:move=sysop]

2015-08-26T12:39:47Z

Protected "5dai" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:39, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5dai is ON HOLD Authors: Ladner, J.E., Altieri, A.S., Kelman, Z. Description: PCNA bound to FEN-1 peptide Category: Unreleased Structures [[Cat...

2015-08-26T12:39:46Z

New page: '''Unreleased structure''' The entry 5dai is ON HOLD Authors: Ladner, J.E., Altieri, A.S., Kelman, Z. Description: PCNA bound to FEN-1 peptide Category: Unreleased Structures [[Cat...

New page

'''Unreleased structure'''

The entry 5dai is ON HOLD

Authors: Ladner, J.E., Altieri, A.S., Kelman, Z.

Description: PCNA bound to FEN-1 peptide
[[Category: Unreleased Structures]]
[[Category: Kelman, Z]]
[[Category: Altieri, A.S]]
[[Category: Ladner, J.E]]