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2pyj
From Proteopedia
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==Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)== | ==Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)== | ||
| - | <StructureSection load='2pyj' size='340' side='right' caption='[[2pyj]], [[Resolution|resolution]] 2.03Å' scene=''> | + | <StructureSection load='2pyj' size='340' side='right'caption='[[2pyj]], [[Resolution|resolution]] 2.03Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2pyj]] is a 8 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2pyj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYJ FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2pyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyj OCA], [https://pdbe.org/2pyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyj RCSB], [https://www.ebi.ac.uk/pdbsum/2pyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyj ProSAT]</span></td></tr> | |
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyj_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyj_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pyj ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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 2pyj" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[DNA polymerase|DNA polymerase]] | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Bacillus | + | [[Category: Bacillus virus phi29]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Berman | + | [[Category: Berman AJ]] |
| - | [[Category: Blanco | + | [[Category: Blanco L]] |
| - | [[Category: Goodman | + | [[Category: Goodman JL]] |
| - | [[Category: Kamtekar | + | [[Category: Kamtekar S]] |
| - | [[Category: Lazaro | + | [[Category: Lazaro JM]] |
| - | [[Category: Salas | + | [[Category: Salas M]] |
| - | [[Category: Steitz | + | [[Category: Steitz TA]] |
| - | [[Category: Vega | + | [[Category: De Vega M]] |
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Current revision
Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)
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