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5nkl

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Current revision (13:03, 15 November 2023) (edit) (undo)
 
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<StructureSection load='5nkl' size='340' side='right'caption='[[5nkl]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='5nkl' size='340' side='right'caption='[[5nkl]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5nkl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NKL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5nkl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] 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=5NKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NKL FirstGlance]. <br>
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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=91R:[[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>91R</scene>, <scene name='pdbligand=91T:[[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>91T</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7&#8491;</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=91N:'>91N</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></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=91N:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(7-thiophen-2-ylimidazo[4,5-b]pyridin-3-yl)oxolan-2-yl]methyl+dihydrogen+phosphate'>91N</scene>, <scene name='pdbligand=91R:[[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>91R</scene>, <scene name='pdbligand=91T:[[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>91T</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkl OCA], [https://pdbe.org/5nkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nkl RCSB], [https://www.ebi.ac.uk/pdbsum/5nkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkl ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkl OCA], [http://pdbe.org/5nkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkl RCSB], [http://www.ebi.ac.uk/pdbsum/5nkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkl ProSAT]</span></td></tr>
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</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
<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>
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[[Category: DNA-directed DNA polymerase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Betz, K]]
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[[Category: Synthetic construct]]
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[[Category: Diederichs, K]]
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[[Category: Thermus aquaticus]]
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[[Category: Hirao, I]]
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[[Category: Betz K]]
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[[Category: Kimoto, M]]
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[[Category: Diederichs K]]
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[[Category: Marx, A]]
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[[Category: Hirao I]]
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[[Category: Artificial base pair]]
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[[Category: Kimoto M]]
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[[Category: Dna polymerase]]
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[[Category: Marx A]]
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[[Category: Ternary complex]]
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[[Category: Transferase]]
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[[Category: Unnatural base pair]]
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Current revision

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP

PDB ID 5nkl

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OCA

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