6qrb - Revision history

OCA at 12:06, 24 January 2024

OCA — Wed, 24 Jan 2024 12:06:56 GMT

←Older revision		Revision as of 12:06, 24 January 2024
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	<StructureSection load='6qrb' size='340' side='right'caption='[[6qrb]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='6qrb' size='340' side='right'caption='[[6qrb]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qrb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6QRB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qrb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus Mycobacteroides abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QRB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=JEQ:5-azanyl-3~~-[1-[~~[(3~{R})-1-(phenylmethyl)piperidin-3-yl~~]~~methyl~~]~~indol-6-yl]-~~1~~~{H}-pyrazole-4-carbonitrile'>JEQ</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]] 1.66Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6nvr\|6nvr]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JEQ:5-azanyl-3-[1-[[(3~{R})-1-(phenylmethyl)piperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JEQ</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmD, MAB_3226c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</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=6qrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrb OCA], [https://pdbe.org/6qrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qrb RCSB], [https://www.ebi.ac.uk/pdbsum/6qrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrb ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/tRNA_~~(~~guanine(37~~)-N(1))-~~methyltransferase tRNA~~ (~~guanine(37~~)-~~N(1))~~-~~methyltransferase~~]~~, with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.~~1~~.1.228 2.1.1.228]~~ </~~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=6qrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrb OCA], [~~http~~://pdbe.org/6qrb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qrb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qrb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrb ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]	+	[https://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abell, C]]	+	[[Category: Mycobacteroides abscessus]]
-	[[Category: Blundell~~, T L~~]]	+	[[Category: Abell C]]
-	[[Category: Coyne~~, A G~~]]	+	[[Category: Blundell TL]]
-	[[Category: Mendes, V]]	+	[[Category: Coyne AG]]
-	[[Category: Thomas~~, S E~~]]	+	[[Category: Mendes V]]
-	[[Category: Whitehouse~~, A J]]~~	+	[[Category: Thomas SE]]
-	~~[[Category: Spout methyltransferase]]~~	+	[[Category: Whitehouse AJ]]
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trmd]]~~	+
-	~~[[Category: Trna methyltransferase~~]]	+

OCA at 06:34, 7 October 2020

OCA — Wed, 07 Oct 2020 06:34:04 GMT

←Older revision		Revision as of 06:34, 7 October 2020
Line 3:		Line 3:
	<StructureSection load='6qrb' size='340' side='right'caption='[[6qrb]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='6qrb' size='340' side='right'caption='[[6qrb]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qrb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QRB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qrb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QRB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JEQ:5-azanyl-3-[1-[[(3~{R})-1-(phenylmethyl)piperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JEQ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JEQ:5-azanyl-3-[1-[[(3~{R})-1-(phenylmethyl)piperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JEQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmD, MAB_3226c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=6qrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrb OCA], [http://pdbe.org/6qrb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qrb RCSB], [http://www.ebi.ac.uk/pdbsum/6qrb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrb 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=6qrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrb OCA], [http://pdbe.org/6qrb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qrb RCSB], [http://www.ebi.ac.uk/pdbsum/6qrb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]		[[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterium abscessus (Mab) is a rapidly growing species of multidrug-resistant nontuberculous mycobacteria that has emerged as a growing threat to individuals with cystic fibrosis and other pre-existing chronic lung diseases. Mab pulmonary infections are difficult, or sometimes impossible, to treat and result in accelerated lung function decline and premature death. There is therefore an urgent need to develop novel antibiotics with improved efficacy. tRNA (m(1)G37) methyltransferase (TrmD) is a promising target for novel antibiotics. It is essential in Mab and other mycobacteria, improving reading frame maintenance on the ribosome to prevent frameshift errors. In this work, a fragment-based approach was employed with the merging of two fragments bound to the active site, followed by structure-guided elaboration to design potent nanomolar inhibitors against Mab TrmD. Several of these compounds exhibit promising activity against mycobacterial species, including Mycobacterium tuberculosis and Mycobacterium leprae in addition to Mab, supporting the use of TrmD as a target for the development of antimycobacterial compounds.
		+
		+	Development of Inhibitors against Mycobacterium abscessus tRNA (m(1)G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.,Whitehouse AJ, Thomas SE, Brown KP, Fanourakis A, Chan DS, Libardo MDJ, Mendes V, Boshoff HIM, Floto RA, Abell C, Blundell TL, Coyne AG J Med Chem. 2019 Aug 8;62(15):7210-7232. doi: 10.1021/acs.jmedchem.9b00809. Epub , 2019 Jul 19. PMID:31282680<ref>PMID:31282680</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6qrb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Abell, C]]		[[Category: Abell, C]]

OCA at 09:46, 18 March 2020

OCA — Wed, 18 Mar 2020 09:46:53 GMT

←Older revision		Revision as of 09:46, 18 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qrb is ~~ON HOLD~~	+	==Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor==
-		+	<StructureSection load='6qrb' size='340' side='right'caption='[[6qrb]], [[Resolution\|resolution]] 1.66Å' scene=''>
-	~~Authors~~: ~~Thomas, S~~.E., ~~Whitehouse, A~~.J., ~~Coyne, A~~.G., ~~Abell~~, C., ~~Mendes, V~~., ~~Blundell, T~~.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6qrb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QRB FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of TrmD, a tRNA~~-~~(N1G37) methyltransferase, from Mycobacterium abscessus~~ in ~~complex with inhibitor~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JEQ:5-azanyl-3-[1-[[(3~{R})-1-(phenylmethyl)piperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JEQ</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>
-	[[Category: Blundell, T.L]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=6qrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrb OCA], [http://pdbe.org/6qrb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qrb RCSB], [http://www.ebi.ac.uk/pdbsum/6qrb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrb ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Abell, C]]
		+	[[Category: Blundell, T L]]
		+	[[Category: Coyne, A G]]
	[[Category: Mendes, V]]		[[Category: Mendes, V]]
-	[[Category: Thomas, S.E]]	+	[[Category: Thomas, S E]]
-	[[Category: ~~Abell~~, C]]	+	[[Category: Whitehouse, A J]]
-	[[Category: ~~Whitehouse, A.J~~]]	+	[[Category: Spout methyltransferase]]
-	[[Category: ~~Coyne, A.G~~]]	+	[[Category: Transferase]]
		+	[[Category: Trmd]]
		+	[[Category: Trna methyltransferase]]

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

OCA — Wed, 27 Feb 2019 13:58:37 GMT

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

←Older revision

Revision as of 13:58, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qrb is ON HOLD Authors: Thomas, S.E., Whitehouse, A.J., Coyne, A.G., Abell, C., Mendes, V., Blundell, T.L. Description: Crystal structure of TrmD,...

OCA — Wed, 27 Feb 2019 13:58:35 GMT

New page: '''Unreleased structure''' The entry 6qrb is ON HOLD Authors: Thomas, S.E., Whitehouse, A.J., Coyne, A.G., Abell, C., Mendes, V., Blundell, T.L. Description: Crystal structure of TrmD,...

New page

'''Unreleased structure'''

The entry 6qrb is ON HOLD

Authors: Thomas, S.E., Whitehouse, A.J., Coyne, A.G., Abell, C., Mendes, V., Blundell, T.L.

Description: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
[[Category: Unreleased Structures]]
[[Category: Blundell, T.L]]
[[Category: Mendes, V]]
[[Category: Thomas, S.E]]
[[Category: Abell, C]]
[[Category: Whitehouse, A.J]]
[[Category: Coyne, A.G]]