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5omf

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Current revision (16:54, 13 December 2023) (edit) (undo)
 
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==Closed, ternary structure of KOD DNA polymerase==
==Closed, ternary structure of KOD DNA polymerase==
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<StructureSection load='5omf' size='340' side='right' caption='[[5omf]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
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<StructureSection load='5omf' size='340' side='right'caption='[[5omf]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5omf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMF FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5omf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1] 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=5OMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OMF 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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.092&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pol, TK0001 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omf OCA], [http://pdbe.org/5omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omf RCSB], [http://www.ebi.ac.uk/pdbsum/5omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omf ProSAT]</span></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=5omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omf OCA], [https://pdbe.org/5omf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5omf RCSB], [https://www.ebi.ac.uk/pdbsum/5omf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5omf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/DPOL_THEKO DPOL_THEKO]] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.
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[https://www.uniprot.org/uniprot/DPOL_THEKO DPOL_THEKO] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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==See Also==
==See Also==
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*[[DNA polymerase|DNA polymerase]]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Betz, K]]
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[[Category: Large Structures]]
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[[Category: Diederichs, K]]
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[[Category: Synthetic construct]]
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[[Category: Kropp, H M]]
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Marx, A]]
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[[Category: Betz K]]
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[[Category: Wirth, J]]
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[[Category: Diederichs K]]
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[[Category: Dna binding protein]]
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[[Category: Kropp HM]]
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[[Category: Dna replication dna polymerase archaea]]
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[[Category: Marx A]]
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[[Category: Wirth J]]

Current revision

Closed, ternary structure of KOD DNA polymerase

PDB ID 5omf

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