1f3f: Difference between revisions

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OCA

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 ==STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX==
-<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.85&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://pdbe.org/1f3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f 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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [https://pdbe.org/1f3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [https://www.ebi.ac.uk/pdbsum/1f3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3f ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/1f3f_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/1f3f_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 17: / Line 20: @@
 </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=1f3f ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-AIDS chemotherapy is limited by inadequate intracellular concentrations of the active triphosphate form of nucleoside analogues, leading to incomplete inhibition of viral replication and the appearance of drug-resistant virus. Drug activation by nucleoside diphosphate kinase and inhibition of HIV-1 reverse transcriptase were studied comparatively. We synthesized analogues with a borano (BH(3)(-)) group on the alpha-phosphate, and found that they are substrates for both enzymes. X-ray structures of complexes with nucleotide diphosphate kinase provided a structural basis for their activation. The complex with d4T triphosphate displayed an intramolecular CH.O bond contributing to catalysis, and the R(p) diastereoisomer of thymidine alpha-boranotriphosphate bound like a normal substrate. Using alpha-(R(p))-boranophosphate derivatives of the clinically relevant compounds AZT and d4T, the presence of the alpha-borano group improved both phosphorylation by nucleotide diphosphate kinase and inhibition of reverse transcription. Moreover, repair of blocked DNA chains by pyrophosphorolysis was reduced significantly in variant reverse transcriptases bearing substitutions found in drug-resistant viruses. Thus, the alpha-borano modification of analogues targeting reverse transcriptase may be of generic value in fighting viral drug resistance.
-Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.,Meyer P, Schneider B, Sarfati S, Deville-Bonne D, Guerreiro C, Boretto J, Janin J, Veron M, Canard B EMBO J. 2000 Jul 17;19(14):3520-9. PMID:10899107<ref>PMID:10899107</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1f3f" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]]
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 11735]]
+[[Category: Dictyostelium discoideum]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Boretto, J]]
+[[Category: Boretto J]]
-[[Category: Canard, B]]
+[[Category: Canard B]]
-[[Category: Deville-Bonne, D]]
+[[Category: Deville-Bonne D]]
-[[Category: Guerreiro, C]]
+[[Category: Guerreiro C]]
-[[Category: Janin, J]]
+[[Category: Janin J]]
-[[Category: Meyer, P]]
+[[Category: Meyer P]]
-[[Category: Sarfati, S]]
+[[Category: Sarfati S]]
-[[Category: Schneider, B]]
+[[Category: Schneider B]]
-[[Category: Veron, M]]
+[[Category: Veron M]]
-[[Category: Anti-hiv nucleoside analogue]]
-[[Category: Ch...o bond]]
-[[Category: Nucleoside diphosphate kinase]]
-[[Category: Phosphorylation]]
-[[Category: Transferase]]