5o0b - Revision history

OCA at 12:18, 22 November 2023

OCA — Wed, 22 Nov 2023 12:18:50 GMT

←Older revision		Revision as of 12:18, 22 November 2023
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	<StructureSection load='5o0b' size='340' side='right'caption='[[5o0b]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='5o0b' size='340' side='right'caption='[[5o0b]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o0b]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5O0B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o0b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus_ATCC_19977 Mycobacteroides abscessus ATCC 19977]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O0B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=9FE:3-bromanyl~~-1~~~{H}-indazole-5-carboxylic+acid'>9FE</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]] 1.735Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Pantetheine~~-~~phosphate_adenylyltransferase Pantetheine~~-~~phosphate adenylyltransferase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9FE:3-bromanyl-1~{H}-indazole-5-carboxylic+acid'>9FE</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=5o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0b OCA], [~~http~~://pdbe.org/5o0b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o0b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o0b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0b 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=5o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0b OCA], [https://pdbe.org/5o0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o0b RCSB], [https://www.ebi.ac.uk/pdbsum/5o0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/COAD_MYCA9 COAD_MYCA9]] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.	+	[https://www.uniprot.org/uniprot/COAD_MYCA9 COAD_MYCA9] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.
	<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: ~~Pantetheine-phosphate adenylyltransferase~~]]	+	[[Category: Mycobacteroides abscessus ATCC 19977]]
-	[[Category: Blaszczyk, M]]	+	[[Category: Blaszczyk M]]
-	[[Category: Blundell~~, T L~~]]	+	[[Category: Blundell TL]]
-	[[Category: Kim~~, S Y~~]]	+	[[Category: Kim SY]]
-	[[Category: Mendes, V]]	+	[[Category: Mendes V]]
-	[[Category: Thomas~~, S E]]~~	+	[[Category: Thomas SE]]
-	~~[[Category: Coenzyme a biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:15, 26 August 2020

OCA — Wed, 26 Aug 2020 12:15:38 GMT

←Older revision		Revision as of 12:15, 26 August 2020
Line 1:		Line 1:

	==Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Bromo-1H-indazole-5-carboxylic acid (Fragment 2)==		==Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Bromo-1H-indazole-5-carboxylic acid (Fragment 2)==
-	<StructureSection load='5o0b' size='340' side='right' caption='[[5o0b]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='5o0b' size='340' side='right'caption='[[5o0b]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o0b]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0B OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O0B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o0b]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5O0B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FE:3-bromanyl-1~{H}-indazole-5-carboxylic+acid'>9FE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9FE:3-bromanyl-1~{H}-indazole-5-carboxylic+acid'>9FE</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pantetheine-phosphate_adenylyltransferase Pantetheine-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pantetheine-phosphate_adenylyltransferase Pantetheine-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3] </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=5o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0b OCA], [http://pdbe.org/5o0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o0b RCSB], [http://www.ebi.ac.uk/pdbsum/5o0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0b ProSAT]</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=5o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0b OCA], [http://pdbe.org/5o0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o0b RCSB], [http://www.ebi.ac.uk/pdbsum/5o0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pantetheine-phosphate adenylyltransferase]]		[[Category: Pantetheine-phosphate adenylyltransferase]]
	[[Category: Blaszczyk, M]]		[[Category: Blaszczyk, M]]

OCA at 11:05, 24 August 2017

OCA — Thu, 24 Aug 2017 11:05:21 GMT

←Older revision		Revision as of 11:05, 24 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o0b is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Bromo-1H-indazole-5-carboxylic acid (Fragment 2)==
		+	<StructureSection load='5o0b' size='340' side='right' caption='[[5o0b]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o0b]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O0B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FE:3-bromanyl-1~{H}-indazole-5-carboxylic+acid'>9FE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pantetheine-phosphate_adenylyltransferase Pantetheine-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3] </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=5o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0b OCA], [http://pdbe.org/5o0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o0b RCSB], [http://www.ebi.ac.uk/pdbsum/5o0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0b ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COAD_MYCA9 COAD_MYCA9]] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.

-	~~Authors~~: Thomas, ~~S.E.~~, Kim, S~~.Y.~~, ~~Mendes, V.~~, Blaszczyk, M., Blundell~~, T~~.L.	+	Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew.,Thomas SE, Mendes V, Kim SY, Malhotra S, Ochoa-Montano B, Blaszczyk M, Blundell TL J Mol Biol. 2017 Aug 18;429(17):2677-2693. doi: 10.1016/j.jmb.2017.06.014. Epub, 2017 Jun 23. PMID:28648615<ref>PMID:28648615</ref>

-	~~Description: Crystal structure~~ of ~~Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3~~-~~Bromo~~-~~1H-indazole-5-carboxylic acid (Fragment 2)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Blundell, T.L]]~~	+	<div class="pdbe-citations 5o0b" style="background-color:#fffaf0;"></div>
-	~~[[Category: Mendes, V]]~~	+	== References ==
-	[[Category: ~~Thomas, S.E~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pantetheine-phosphate adenylyltransferase]]
	[[Category: Blaszczyk, M]]		[[Category: Blaszczyk, M]]
-	[[Category: Kim, S.Y]]	+	[[Category: Blundell, T L]]
		+	[[Category: Kim, S Y]]
		+	[[Category: Mendes, V]]
		+	[[Category: Thomas, S E]]
		+	[[Category: Coenzyme a biosynthesis]]
		+	[[Category: Transferase]]

OCA: Protected "5o0b" [edit=sysop:move=sysop]

OCA — Wed, 24 May 2017 10:05:34 GMT

Protected "5o0b" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:05, 24 May 2017

OCA: New page: '''Unreleased structure''' The entry 5o0b is ON HOLD until Paper Publication Authors: Thomas, S.E., Kim, S.Y., Mendes, V., Blaszczyk, M., Blundell, T.L. Description: Crystal structure ...

OCA — Wed, 24 May 2017 10:05:33 GMT

New page: '''Unreleased structure''' The entry 5o0b is ON HOLD until Paper Publication Authors: Thomas, S.E., Kim, S.Y., Mendes, V., Blaszczyk, M., Blundell, T.L. Description: Crystal structure ...

New page

'''Unreleased structure'''

The entry 5o0b is ON HOLD until Paper Publication

Authors: Thomas, S.E., Kim, S.Y., Mendes, V., Blaszczyk, M., Blundell, T.L.

Description: Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Bromo-1H-indazole-5-carboxylic acid (Fragment 2)
[[Category: Unreleased Structures]]
[[Category: Blundell, T.L]]
[[Category: Mendes, V]]
[[Category: Thomas, S.E]]
[[Category: Blaszczyk, M]]
[[Category: Kim, S.Y]]