4b6c: Difference between revisions

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 ==Structure of the M. smegmatis GyrB ATPase domain in complex with an aminopyrazinamide==
-<StructureSection load='4b6c' size='340' side='right' caption='[[4b6c]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='4b6c' size='340' side='right'caption='[[4b6c]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b6c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B6C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B6C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b6c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B6C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B5U:6-(3,4-DIMETHYLPHENYL)-3-[[4-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]PHENYL]AMINO]PYRAZINE-2-CARBOXAMIDE'>B5U</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.2&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B5U:6-(3,4-DIMETHYLPHENYL)-3-[[4-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]PHENYL]AMINO]PYRAZINE-2-CARBOXAMIDE'>B5U</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=4b6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b6c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4b6c RCSB], [http://www.ebi.ac.uk/pdbsum/4b6c PDBsum]</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=4b6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b6c OCA], [https://pdbe.org/4b6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b6c RCSB], [https://www.ebi.ac.uk/pdbsum/4b6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b6c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GYRB_MYCSM GYRB_MYCSM]] 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.
+[https://www.uniprot.org/uniprot/GYRB_MYCSM GYRB_MYCSM] 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.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Aminopyrazinamides originated from a high throughput screen targeting the Mycobacterium smegmatis (Msm) GyrB ATPase. This series displays chemical tractability, robust structure-activity relationship, and potent antitubercular activity. The crystal structure of Msm GyrB in complex with one of the aminopyrazinamides revealed promising attributes of specificity against other broad spectrum pathogens and selectivity against eukaryotic kinases due to novel interactions at hydrophobic pocket, unlike other known GyrB inhibitors. The aminopyrazinamides display excellent mycobacterial kill under in vitro, intracellular, and hypoxic conditions.
-Aminopyrazinamides: Novel and Specific GyrB Inhibitors that Kill Replicating and Nonreplicating Mycobacterium tuberculosis.,Shirude PS, Madhavapeddi P, Tucker JA, Murugan K, Patil V, Basavarajappa H, Raichurkar AV, Humnabadkar V, Hussein S, Sharma S, Ramya VK, Narayan CB, Balganesh TS, Sambandamurthy VK ACS Chem Biol. 2012 Dec 31. PMID:23268609<ref>PMID:23268609</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Gyrase|Gyrase]]
+*[[Gyrase 3D Structures|Gyrase 3D Structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Mycobacterium smegmatis]]
+[[Category: Large Structures]]
-[[Category: Basu, R]]
+[[Category: Mycolicibacterium smegmatis]]
-[[Category: Ghorpade, S]]
+[[Category: Basu R]]
-[[Category: Hussein, S]]
+[[Category: Ghorpade S]]
-[[Category: Madhavapeddi, P]]
+[[Category: Hussein S]]
-[[Category: Shirude, P S]]
+[[Category: Madhavapeddi P]]
-[[Category: Tucker, J A]]
+[[Category: Shirude PS]]
-[[Category: Dna topoisomerase]]
+[[Category: Tucker JA]]
-[[Category: Inhibitor]]
-[[Category: Isomerase]]