3fcf - Revision history

OCA at 00:30, 28 December 2023

OCA — Thu, 28 Dec 2023 00:30:48 GMT

←Older revision		Revision as of 00:30, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='3fcf' size='340' side='right'caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='3fcf' size='340' side='right'caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fcf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fcf]] is a 1 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=3FCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 1.84Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [https://pdbe.org/3fcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [https://www.ebi.ac.uk/pdbsum/3fcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fcf 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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [https://pdbe.org/3fcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [https://www.ebi.ac.uk/pdbsum/3fcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fcf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>	+	[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.	+	[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Amzel~~, L M~~]]	+	[[Category: Amzel LM]]
-	[[Category: Bianchet~~, M A~~]]	+	[[Category: Bianchet MA]]
-	[[Category: Chung, S]]	+	[[Category: Chung S]]
-	[[Category: Parker~~, J B~~]]	+	[[Category: Parker JB]]
-	[[Category: Stivers~~, J T]]~~	+	[[Category: Stivers JT]]
-	~~[[Category: Alternative splicing]]~~	+
-	~~[[Category: Disease mutation]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Host-virus interaction]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mitochondrion]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Transit peptide]]~~	+
-	~~[[Category: Uracil]]~~	+
-	~~[[Category: Uracil dna glycosylase~~]]	+

OCA at 07:57, 2 March 2022

OCA — Wed, 02 Mar 2022 07:57:39 GMT

←Older revision		Revision as of 07:57, 2 March 2022
Line 1:		Line 1:

	==Complex of UNG2 and a fragment-based designed inhibitor==		==Complex of UNG2 and a fragment-based designed inhibitor==
-	<StructureSection load='3fcf' size='340' side='right' caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='3fcf' size='340' side='right'caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fcf]] is a 1 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=3FCF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fcf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([https://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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [~~http~~://pdbe.org/3fcf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fcf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fcf 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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [https://pdbe.org/3fcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [https://www.ebi.ac.uk/pdbsum/3fcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fcf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[~~http~~://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>	+	[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.	+	[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/3fcf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/3fcf_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 32:		Line 32:
	</div>		</div>
	<div class="pdbe-citations 3fcf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3fcf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Amzel, L M]]		[[Category: Amzel, L M]]
	[[Category: Bianchet, M A]]		[[Category: Bianchet, M A]]

OCA at 06:38, 1 November 2017

OCA — Wed, 01 Nov 2017 06:38:34 GMT

←Older revision		Revision as of 06:38, 1 November 2017
Line 1:		Line 1:
		+
	==Complex of UNG2 and a fragment-based designed inhibitor==		==Complex of UNG2 and a fragment-based designed inhibitor==
	<StructureSection load='3fcf' size='340' side='right' caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='3fcf' size='340' side='right' caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [http://pdbe.org/3fcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [http://www.ebi.ac.uk/pdbsum/3fcf 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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [http://pdbe.org/3fcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [http://www.ebi.ac.uk/pdbsum/3fcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fcf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 31:		Line 32:
	</div>		</div>
	<div class="pdbe-citations 3fcf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3fcf" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]
-	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 45:		Line 42:
	[[Category: Parker, J B]]		[[Category: Parker, J B]]
	[[Category: Stivers, J T]]		[[Category: Stivers, J T]]
		+	[[Category: Alternative splicing]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]
	[[Category: Dna damage]]		[[Category: Dna damage]]

OCA at 15:30, 8 February 2016

OCA — Mon, 08 Feb 2016 15:30:19 GMT

←Older revision		Revision as of 15:30, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3fcf' size='340' side='right' caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='3fcf' size='340' side='right' caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fcf]] is a 1 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=3FCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FCF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [http://www.ebi.ac.uk/pdbsum/3fcf 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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [http://pdbe.org/3fcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [http://www.ebi.ac.uk/pdbsum/3fcf PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 20:
	<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=3fcf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	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 3fcf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Amzel, L M]]		[[Category: Amzel, L M]]
	[[Category: Bianchet, M A]]		[[Category: Bianchet, M A]]

OCA at 14:53, 5 January 2015

OCA — Mon, 05 Jan 2015 14:53:13 GMT

←Older revision		Revision as of 14:53, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3fcf~~\| ~~PDB~~=3fcf \| ~~SCENE~~= }}	+	==Complex of UNG2 and a fragment-based designed inhibitor==
-	===~~Complex~~ of ~~UNG2~~ and a ~~fragment~~-~~based designed inhibitor~~===	+	<StructureSection load='3fcf' size='340' side='right' caption='[[3fcf]], [[Resolution\|resolution]] 1.84Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19396178}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FCF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC+ACID'>FCF</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fci\|3fci]], [[3fck\|3fck]], [[3fcl\|3fcl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG, DGU, UNG1, UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fcf RCSB], [http://www.ebi.ac.uk/pdbsum/3fcf PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[http://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
		+	== 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/fc/3fcf_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The linking together of molecular fragments that bind to adjacent sites on an enzyme can lead to high-affinity inhibitors. Ideally, this strategy would use linkers that do not perturb the optimal binding geometries of the fragments and do not have excessive conformational flexibility that would increase the entropic penalty of binding. In reality, these aims are seldom realized owing to limitations in linker chemistry. Here we systematically explore the energetic and structural effects of rigid and flexible linkers on the binding of a fragment-based inhibitor of human uracil DNA glycosylase. Analysis of the free energies of binding in combination with cocrystal structures shows that the flexibility and strain of a given linker can have a substantial impact on binding affinity even when the binding fragments are optimally positioned. Such effects are not apparent from inspection of structures and underscore the importance of linker optimization in fragment-based drug discovery efforts.

-	~~==Disease==~~	+	Impact of linker strain and flexibility in the design of a fragment-based inhibitor.,Chung S, Parker JB, Bianchet M, Amzel LM, Stivers JT Nat Chem Biol. 2009 Jun;5(6):407-13. Epub 2009 Apr 26. PMID:19396178<ref>PMID:19396178</ref>
-	~~[[http://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects~~ in ~~UNG are a cause~~ of ~~immunodeficiency with hyper~~-~~IgM type~~ 5 (~~HIGM5~~) ~~[MIM~~:~~[http://omim~~.~~org/entry/608106 608106]]~~. ~~A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>~~PMID:~~12958596</ref>~~<ref>PMID:~~15967827~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www~~.~~uniprot~~.~~org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result~~ of ~~misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine~~.	+	</div>
-		+
-	~~==About this Structure==~~	+
-	~~[[3fcf]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
-		+	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
-	==~~Reference~~==	+	== References ==
-	~~<ref group="xtra">PMID:019396178</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Amzel, L M.]]	+	[[Category: Amzel, L M]]
-	[[Category: Bianchet, M A.]]	+	[[Category: Bianchet, M A]]
-	[[Category: Chung, S.]]	+	[[Category: Chung, S]]
-	[[Category: Parker, J B.]]	+	[[Category: Parker, J B]]
-	[[Category: Stivers, J T.]]	+	[[Category: Stivers, J T]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]
	[[Category: Dna damage]]		[[Category: Dna damage]]

OCA at 17:50, 24 March 2013

OCA — Sun, 24 Mar 2013 17:50:30 GMT

←Older revision		Revision as of 17:50, 24 March 2013
Line 1:		Line 1:
-	[[Image:3fcf.png\|left\|200px]]
-
	{{STRUCTURE_3fcf\| PDB=3fcf \| SCENE= }}		{{STRUCTURE_3fcf\| PDB=3fcf \| SCENE= }}
-
	===Complex of UNG2 and a fragment-based designed inhibitor===		===Complex of UNG2 and a fragment-based designed inhibitor===
		+	{{ABSTRACT_PUBMED_19396178}}

-	~~{{ABSTRACT_PUBMED_19396178}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[http://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref><ref>PMID:15967827</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019396178</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019396178</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Amzel, L M.]]		[[Category: Amzel, L M.]]

OCA at 10:36, 20 October 2012

OCA — Sat, 20 Oct 2012 10:36:37 GMT

←Older revision		Revision as of 10:36, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3fcf]] is a 1 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].	+	[[3fcf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].

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

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

OCA — Thu, 26 Jul 2012 02:41:17 GMT

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

←Older revision

Revision as of 02:41, 26 July 2012

OCA at 02:41, 26 July 2012

OCA — Thu, 26 Jul 2012 02:41:16 GMT

←Older revision		Revision as of 02:41, 26 July 2012
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-	{{Seed}}
	[[Image:3fcf.png\|left\|200px]]		[[Image:3fcf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fcf", 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),
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	{{STRUCTURE_3fcf\| PDB=3fcf \| SCENE= }}		{{STRUCTURE_3fcf\| PDB=3fcf \| SCENE= }}

	===Complex of UNG2 and a fragment-based designed inhibitor===		===Complex of UNG2 and a fragment-based designed inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19396178}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_19396178}}		{{ABSTRACT_PUBMED_19396178}}

	==About this Structure==		==About this Structure==
-	~~3FCF~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].	+	[[3fcf]] is a 1 chain structure of [[DNA glycosylate]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].
		+
		+	==See Also==
		+	*[[DNA glycosylate\|DNA glycosylate]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19396178~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019396178</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Amzel, L M.]]		[[Category: Amzel, L M.]]
Line 30:		Line 21:
	[[Category: Parker, J B.]]		[[Category: Parker, J B.]]
	[[Category: Stivers, J T.]]		[[Category: Stivers, J T.]]
-	[[Category: Alternative splicing]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
Line 43:		Line 33:
	[[Category: Uracil]]		[[Category: Uracil]]
	[[Category: Uracil dna glycosylase]]		[[Category: Uracil dna glycosylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 3 09:38:45 2009''

OCA at 06:38, 3 June 2009

OCA — Wed, 03 Jun 2009 06:38:46 GMT

←Older revision		Revision as of 06:38, 3 June 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3fcf.~~jpg~~\|left\|200px]]	+	[[Image:3fcf.png\|left\|200px]]

	<!--		<!--
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	===Complex of UNG2 and a fragment-based designed inhibitor===		===Complex of UNG2 and a fragment-based designed inhibitor===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19396178}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19396178 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19396178}}

	==About this Structure==		==About this Structure==
	3FCF is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].		3FCF is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19396178</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Amzel, L M.]]		[[Category: Amzel, L M.]]
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	[[Category: Uracil dna glycosylase]]		[[Category: Uracil dna glycosylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 30 19~~:17:30 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 3 09:38:45 2009''