4urm - Revision history

OCA at 11:22, 9 May 2024

OCA — Thu, 09 May 2024 11:22:39 GMT

←Older revision		Revision as of 11:22, 9 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4urm]] is a 4 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=4URM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4URM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4urm]] is a 4 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=4URM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4URM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</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]] 2.94Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [https://pdbe.org/4urm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [https://www.ebi.ac.uk/pdbsum/4urm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4urm 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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [https://pdbe.org/4urm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [https://www.ebi.ac.uk/pdbsum/4urm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4urm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:34, 29 March 2023

OCA — Wed, 29 Mar 2023 07:34:20 GMT

←Older revision		Revision as of 07:34, 29 March 2023
Line 3:		Line 3:
	<StructureSection load='4urm' size='340' side='right'caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>		<StructureSection load='4urm' size='340' side='right'caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4urm]] is a 4 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=4URM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4URM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4urm]] is a 4 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=4URM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4URM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [https://pdbe.org/4urm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [https://www.ebi.ac.uk/pdbsum/4urm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4urm 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/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [~~http~~://pdbe.org/4urm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4urm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4urm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GYRB_STAAU GYRB_STAAU]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.[HAMAP-Rule:MF_01898]	+	[https://www.uniprot.org/uniprot/GYRB_STAAU GYRB_STAAU] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.[HAMAP-Rule:MF_01898]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Gyrase\|Gyrase]]	+	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukuda, Y]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: Kishii, R]]	+	[[Category: Fukuda Y]]
-	[[Category: Lu, J]]	+	[[Category: Kishii R]]
-	[[Category: Lumb~~, K J~~]]	+	[[Category: Lu J]]
-	[[Category: Patel, S]]	+	[[Category: Lumb KJ]]
-	[[Category: Sharma, N]]	+	[[Category: Patel S]]
-	[[Category: Singh~~, S B~~]]	+	[[Category: Sharma N]]
-	[[Category: Soisson, S]]	+	[[Category: Singh SB]]
-	[[Category: Takei, M]]	+	[[Category: Soisson S]]
-	~~[[Category: Antibiotic]]~~	+	[[Category: Takei M]]
-	~~[[Category: Gyrase]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Natural product]]~~	+
-	~~[[Category: Topoisomerase iv~~]]	+

OCA at 08:59, 21 May 2019

OCA — Tue, 21 May 2019 08:59:51 GMT

←Older revision		Revision as of 08:59, 21 May 2019
Line 1:		Line 1:

	==Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin==		==Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin==
-	<StructureSection load='4urm' size='340' side='right' caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>	+	<StructureSection load='4urm' size='340' side='right'caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4urm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4URM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4URM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4urm]] is a 4 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=4URM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4URM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>
Line 27:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fukuda, Y]]		[[Category: Fukuda, Y]]
	[[Category: Kishii, R]]		[[Category: Kishii, R]]

OCA at 18:25, 4 August 2016

OCA — Thu, 04 Aug 2016 18:25:40 GMT

←Older revision		Revision as of 18:25, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin==		==Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin==
	<StructureSection load='4urm' size='340' side='right' caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>		<StructureSection load='4urm' size='340' side='right' caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [http://www.ebi.ac.uk/pdbsum/4urm 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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [http://pdbe.org/4urm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [http://www.ebi.ac.uk/pdbsum/4urm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4urm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4urm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gyrase\|Gyrase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:53, 25 December 2014

OCA — Thu, 25 Dec 2014 11:53:18 GMT

←Older revision		Revision as of 11:53, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4urm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4URM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4URM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4urm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4URM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4URM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [http://www.ebi.ac.uk/pdbsum/4urm 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=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [http://www.ebi.ac.uk/pdbsum/4urm PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GYRB_STAAU GYRB_STAAU]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.[HAMAP-Rule:MF_01898]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fukuda, Y.]]	+	[[Category: Fukuda, Y]]
-	[[Category: Kishii, R.]]	+	[[Category: Kishii, R]]
-	[[Category: Lu, J.]]	+	[[Category: Lu, J]]
-	[[Category: Lumb, K J.]]	+	[[Category: Lumb, K J]]
-	[[Category: Patel, S.]]	+	[[Category: Patel, S]]
-	[[Category: Sharma, N.]]	+	[[Category: Sharma, N]]
-	[[Category: Singh, S B.]]	+	[[Category: Singh, S B]]
-	[[Category: Soisson, S.]]	+	[[Category: Soisson, S]]
-	[[Category: Takei, M.]]	+	[[Category: Takei, M]]
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Gyrase]]		[[Category: Gyrase]]

OCA at 07:42, 30 July 2014

OCA — Wed, 30 Jul 2014 07:42:51 GMT

←Older revision		Revision as of 07:42, 30 July 2014
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-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin==
		+	<StructureSection load='4urm' size='340' side='right' caption='[[4urm]], [[Resolution\|resolution]] 2.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4urm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4URM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4URM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAM:(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL+2,6-DIDEOXY-3-C-[(1S)-1-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE'>XAM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4url\|4url]], [[4urn\|4urn]], [[4uro\|4uro]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4urm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4urm RCSB], [http://www.ebi.ac.uk/pdbsum/4urm PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial resistance to antibiotics continues to pose serious challenges as the discovery rate for new antibiotics fades. Kibdelomycin is one of the rare, novel, natural product antibiotics discovered recently that inhibits the bacterial DNA synthesis enzymes gyrase and topoisomerase IV. It is a broad-spectrum, Gram-positive antibiotic without cross-resistance to known gyrase inhibitors, including clinically effective quinolones. To understand its mechanism of action, binding mode, and lack of cross-resistance, we have co-crystallized kibdelomycin and novobiocin with the N-terminal domains of Staphylococcus aureus gyrase B (24 kDa) and topo IV (ParE, 24 and 43 kDa). Kibdelomycin shows a unique "dual-arm", U-shaped binding mode in both crystal structures. The pyrrolamide moiety in the lower part of kibdelomycin penetrates deeply into the ATP-binding site pocket, whereas the isopropyl-tetramic acid and sugar moiety of the upper part thoroughly engage in polar interactions with a surface patch of the protein. The isoproramic acid (1,3-dioxopyrrolidine) and a tetrahydropyran acetate group (Sugar A) make polar contact with a surface area consisting of helix alpha4 and the flexible loop connecting helices alpha3 and alpha4. The two arms are connected together by a rigid decalin linker that makes van del Waals contacts with the protein backbone. This "dual-arm", U-shaped, multicontact binding mode of kibdelomycin is unique and distinctively different from binding modes of other known gyrase inhibitors (e.g., coumarins and quinolones), which explains its lack of cross-resistance and low frequency of resistance. The crystal structures reported in this paper should enable design and discovery of analogues with better properties and antibacterial spectrum.

-	~~The entry 4urm is ON HOLD until Paper Publication~~	+	Structures of Kibdelomycin Bound to Staphylococcus aureus GyrB and ParE Showed a Novel U-Shaped Binding Mode.,Lu J, Patel S, Sharma N, Soisson SM, Kishii R, Takei M, Fukuda Y, Lumb KJ, Singh SB ACS Chem Biol. 2014 Jul 3. PMID:24992706<ref>PMID:24992706</ref>

-	~~Authors: Lu~~, J.~~, Patel,~~ S.~~, Sharma, N~~., ~~Soisson, S~~., Kishii, R., ~~Takei, M~~.~~, Fukuda, Y.,~~ Lumb, K.J., Singh, S.B.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fukuda, Y.]]
		+	[[Category: Kishii, R.]]
		+	[[Category: Lu, J.]]
		+	[[Category: Lumb, K J.]]
		+	[[Category: Patel, S.]]
		+	[[Category: Sharma, N.]]
		+	[[Category: Singh, S B.]]
		+	[[Category: Soisson, S.]]
		+	[[Category: Takei, M.]]
		+	[[Category: Antibiotic]]
		+	[[Category: Gyrase]]
		+	[[Category: Isomerase]]
		+	[[Category: Natural product]]
		+	[[Category: Topoisomerase iv]]

OCA at 07:28, 23 July 2014

OCA — Wed, 23 Jul 2014 07:28:28 GMT

←Older revision		Revision as of 07:28, 23 July 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4urm is ON HOLD	+	The entry 4urm is ON HOLD until Paper Publication

	Authors: Lu, J., Patel, S., Sharma, N., Soisson, S., Kishii, R., Takei, M., Fukuda, Y., Lumb, K.J., Singh, S.B.		Authors: Lu, J., Patel, S., Sharma, N., Soisson, S., Kishii, R., Takei, M., Fukuda, Y., Lumb, K.J., Singh, S.B.

	Description: Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin		Description: Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin

OCA: Protected "4urm" [edit=sysop:move=sysop]

OCA — Wed, 09 Jul 2014 07:02:59 GMT

Protected "4urm" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:02, 9 July 2014

OCA: New page: '''Unreleased structure''' The entry 4urm is ON HOLD Authors: Lu, J., Patel, S., Sharma, N., Soisson, S., Kishii, R., Takei, M., Fukuda, Y., Lumb, K.J., Singh, S.B. Description: Crysta...

OCA — Wed, 09 Jul 2014 07:02:59 GMT

New page: '''Unreleased structure''' The entry 4urm is ON HOLD Authors: Lu, J., Patel, S., Sharma, N., Soisson, S., Kishii, R., Takei, M., Fukuda, Y., Lumb, K.J., Singh, S.B. Description: Crysta...

New page

'''Unreleased structure'''

The entry 4urm is ON HOLD

Authors: Lu, J., Patel, S., Sharma, N., Soisson, S., Kishii, R., Takei, M., Fukuda, Y., Lumb, K.J., Singh, S.B.

Description: Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin