5fpo - Revision history

OCA at 13:17, 26 July 2023

OCA — Wed, 26 Jul 2023 13:17:42 GMT

←Older revision		Revision as of 13:17, 26 July 2023
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	<StructureSection load='5fpo' size='340' side='right'caption='[[5fpo]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5fpo' size='340' side='right'caption='[[5fpo]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fpo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FPO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fpo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FPO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=10L:1H~~-~~INDAZOL-7-AMINE'>10L</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]] 1.83Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fp5\|5fp5]], [[5fp6\|5fp6]], [[5fpd\|5fpd]], [[5fpe\|5fpe]], [[5fpm\|5fpm]], [[5fpn\|5fpn]], [[5fpr\|5fpr]], [[5fps\|5fps]], [[5fpt\|5fpt]], [[5fpy\|5fpy]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10L:1H-INDAZOL-7-AMINE'>10L</scene></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=5fpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpo OCA], [~~http~~://pdbe.org/5fpo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fpo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fpo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fpo 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=5fpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpo OCA], [https://pdbe.org/5fpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fpo RCSB], [https://www.ebi.ac.uk/pdbsum/5fpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fpo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DNLJ_STAAU DNLJ_STAAU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jhoti, H]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: Ludlow~~, R F~~]]	+	[[Category: Jhoti H]]
-	[[Category: Pathuri, P]]	+	[[Category: Ludlow RF]]
-	[[Category: Saini~~, H K~~]]	+	[[Category: Pathuri P]]
-	[[Category: Tickle~~, I J~~]]	+	[[Category: Saini HK]]
-	[[Category: Tisi, D]]	+	[[Category: Tickle IJ]]
-	[[Category: Verdonk, M]]	+	[[Category: Tisi D]]
-	[[Category: Williams~~, P A]]~~	+	[[Category: Verdonk M]]
-	~~[[Category: Alternate binding site]]~~	+	[[Category: Williams PA]]
-	~~[[Category: Antibiotic design]]~~	+
-	~~[[Category: At4213]]~~	+
-	~~[[Category: Fragment screening]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Protein-ligand complex~~]]	+

OCA at 07:30, 6 May 2020

OCA — Wed, 06 May 2020 07:30:54 GMT

←Older revision		Revision as of 07:30, 6 May 2020
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		+
	==Structure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213) in an alternate binding site.==		==Structure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213) in an alternate binding site.==
-	<StructureSection load='5fpo' size='340' side='right' caption='[[5fpo]], [[Resolution\|resolution]] 1.83Å' scene=''>	+	<StructureSection load='5fpo' size='340' side='right'caption='[[5fpo]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fpo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FPO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fpo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FPO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=10L:1H-INDAZOL-7-AMINE'>10L</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10L:1H-INDAZOL-7-AMINE'>10L</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fp5\|5fp5]], [[5fp6\|5fp6]], [[5fpd\|5fpd]], [[5fpe\|5fpe]], [[5fpm\|5fpm]], [[5fpn\|5fpn]], [[5fpr\|5fpr]], [[5fps\|5fps]], [[5fpt\|5fpt]], [[5fpy\|5fpy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fp5\|5fp5]], [[5fp6\|5fp6]], [[5fpd\|5fpd]], [[5fpe\|5fpe]], [[5fpm\|5fpm]], [[5fpn\|5fpn]], [[5fpr\|5fpr]], [[5fps\|5fps]], [[5fpt\|5fpt]], [[5fpy\|5fpy]]</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=5fpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpo OCA], [http://pdbe.org/5fpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fpo RCSB], [http://www.ebi.ac.uk/pdbsum/5fpo PDBsum]</span></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=5fpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpo OCA], [http://pdbe.org/5fpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fpo RCSB], [http://www.ebi.ac.uk/pdbsum/5fpo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fpo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5fpo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fpo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Jhoti, H]]		[[Category: Jhoti, H]]
	[[Category: Ludlow, R F]]		[[Category: Ludlow, R F]]

OCA at 12:43, 23 December 2015

OCA — Wed, 23 Dec 2015 12:43:22 GMT

←Older revision		Revision as of 12:43, 23 December 2015
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-	'''~~Unreleased~~ structure'''	+	==Structure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213) in an alternate binding site.==
		+	<StructureSection load='5fpo' size='340' side='right' caption='[[5fpo]], [[Resolution\|resolution]] 1.83Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fpo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FPO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=10L:1H-INDAZOL-7-AMINE'>10L</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fp5\|5fp5]], [[5fp6\|5fp6]], [[5fpd\|5fpd]], [[5fpe\|5fpe]], [[5fpm\|5fpm]], [[5fpn\|5fpn]], [[5fpr\|5fpr]], [[5fps\|5fps]], [[5fpt\|5fpt]], [[5fpy\|5fpy]]</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=5fpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fpo OCA], [http://pdbe.org/5fpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fpo RCSB], [http://www.ebi.ac.uk/pdbsum/5fpo PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.

-	~~The entry 5fpo is ON HOLD~~	+	Detection of secondary binding sites in proteins using fragment screening.,Ludlow RF, Verdonk ML, Saini HK, Tickle IJ, Jhoti H Proc Natl Acad Sci U S A. 2015 Dec 11. pii: 201518946. PMID:26655740<ref>PMID:26655740</ref>

-	~~Authors: JHOTI~~, H.~~, LUDLOW, R~~.~~F., PATHURI, P., SAINI, H.K., TICKLE, I.J., TISI, D., VERDONK, M., WILLIAMS, P.A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Structure of Bacterial DNA Ligase with small~~-~~molecule ligand 1H~~-~~indazol-7-amine (AT4213) in an alternate binding site.~~	+	<div class="pdbe-citations 5fpo" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Williams~~, P.A]]	+	<references/>
-	[[Category: Tickle, I.J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Jhoti, H]]
		+	[[Category: Ludlow, R F]]
		+	[[Category: Pathuri, P]]
		+	[[Category: Saini, H K]]
		+	[[Category: Tickle, I J]]
	[[Category: Tisi, D]]		[[Category: Tisi, D]]
-	[[Category: Saini, H.K]]
	[[Category: Verdonk, M]]		[[Category: Verdonk, M]]
-	[[Category: ~~Ludlow~~, ~~R.F~~]]	+	[[Category: Williams, P A]]
-	[[Category: ~~Pathuri, P~~]]	+	[[Category: Alternate binding site]]
-	[[Category: ~~Jhoti, H~~]]	+	[[Category: Antibiotic design]]
		+	[[Category: At4213]]
		+	[[Category: Fragment screening]]
		+	[[Category: Ligase]]
		+	[[Category: Protein-ligand complex]]

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

OCA — Wed, 09 Dec 2015 12:52:45 GMT

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

←Older revision

Revision as of 12:52, 9 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fpo is ON HOLD Authors: JHOTI, H., LUDLOW, R.F., PATHURI, P., SAINI, H.K., TICKLE, I.J., TISI, D., VERDONK, M., WILLIAMS, P.A. Description: Struct...

OCA — Wed, 09 Dec 2015 12:52:44 GMT

New page: '''Unreleased structure''' The entry 5fpo is ON HOLD Authors: JHOTI, H., LUDLOW, R.F., PATHURI, P., SAINI, H.K., TICKLE, I.J., TISI, D., VERDONK, M., WILLIAMS, P.A. Description: Struct...

New page

'''Unreleased structure'''

The entry 5fpo is ON HOLD

Authors: JHOTI, H., LUDLOW, R.F., PATHURI, P., SAINI, H.K., TICKLE, I.J., TISI, D., VERDONK, M., WILLIAMS, P.A.

Description: Structure of Bacterial DNA Ligase with small-molecule ligand 1H-indazol-7-amine (AT4213) in an alternate binding site.
[[Category: Unreleased Structures]]
[[Category: Williams, P.A]]
[[Category: Tickle, I.J]]
[[Category: Tisi, D]]
[[Category: Saini, H.K]]
[[Category: Verdonk, M]]
[[Category: Ludlow, R.F]]
[[Category: Pathuri, P]]
[[Category: Jhoti, H]]