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5cdo

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Current revision (12:00, 14 June 2023) (edit) (undo)
 
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<StructureSection load='5cdo' size='340' side='right'caption='[[5cdo]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
<StructureSection load='5cdo' size='340' side='right'caption='[[5cdo]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5cdo]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Staan Staan]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CDO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5cdo]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_N315 Staphylococcus aureus subsp. aureus N315] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CDO FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=50M:(2R,4S,4AS,5R)-6-HYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5-PYRIMIDINE]-2,4(3H)-DIONE'>50M</scene>, <scene name='pdbligand=53L:(2R,4S,4AS,5S)-6-HYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5-PYRIMIDINE]-2,4(3H)-DIONE'>53L</scene>, <scene name='pdbligand=53M:(2R,4S,4AS)-4,6-DIHYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5-PYRIMIDIN]-2-ONE'>53M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=50M:(2R,4S,4AS,5R)-6-HYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5-PYRIMIDINE]-2,4(3H)-DIONE'>50M</scene>, <scene name='pdbligand=53L:(2R,4S,4AS,5S)-6-HYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5-PYRIMIDINE]-2,4(3H)-DIONE'>53L</scene>, <scene name='pdbligand=53M:(2R,4S,4AS)-4,6-DIHYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5-PYRIMIDIN]-2-ONE'>53M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5cdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdo OCA], [https://pdbe.org/5cdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cdo RCSB], [https://www.ebi.ac.uk/pdbsum/5cdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdo ProSAT]</span></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrA, SA0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 STAAN]), gyrB, SA0005 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 STAAN])</td></tr>
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<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>
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<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=5cdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdo OCA], [http://pdbe.org/5cdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdo RCSB], [http://www.ebi.ac.uk/pdbsum/5cdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdo ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/GYRA_STAAN GYRA_STAAN]] 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_01897] [[http://www.uniprot.org/uniprot/GYRB_STAAN GYRB_STAAN]] 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 (By similarity).
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[https://www.uniprot.org/uniprot/GYRA_STAAN GYRA_STAAN] 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_01897]
<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]]
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[[Category: Staan]]
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[[Category: Staphylococcus aureus subsp. aureus N315]]
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[[Category: Bax, B D]]
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[[Category: Synthetic construct]]
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[[Category: Chan, P F]]
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[[Category: Bax BD]]
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[[Category: Srikannathasan, V]]
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[[Category: Chan PF]]
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[[Category: Antibacterial]]
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[[Category: Srikannathasan V]]
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[[Category: Inhibitor]]
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[[Category: Isomerase]]
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[[Category: Type iia topoisomerase]]
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Current revision

3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA

PDB ID 5cdo

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