1ki4: Difference between revisions

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 ==CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-BROMOTHIENYLDEOXYURIDINE==
-<StructureSection load='1ki4' size='340' side='right' caption='[[1ki4]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
+<StructureSection load='1ki4' size='340' side='right'caption='[[1ki4]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ki4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KI4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ki4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KI4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTD:5-BROMOTHIENYLDEOXYURIDINE'>BTD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.34&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTD:5-BROMOTHIENYLDEOXYURIDINE'>BTD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=1ki4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ki4 OCA], [https://pdbe.org/1ki4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ki4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ki4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ki4 ProSAT]</span></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=1ki4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ki4 OCA], [http://pdbe.org/1ki4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ki4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ki4 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).
+[https://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).
 == 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/ki/1ki4_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ki/1ki4_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / 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=1ki4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Antiherpes therapies are principally targeted at viral thymidine kinases and utilize nucleoside analogs, the triphosphates of which are inhibitors of viral DNA polymerase or result in toxic effects when incorporated into DNA. The most frequently used drug, aciclovir (Zovirax), is a relatively poor substrate for thymidine kinase and high-resolution structural information on drugs and other molecules binding to the target is therefore important for the design of novel and more potent chemotherapy, both in antiherpes treatment and in gene therapy systems where thymidine kinase is expressed. Here, we report for the first time the binary complexes of HSV-1 thymidine kinase (TK) with the drug molecules aciclovir and penciclovir, determined by X-ray crystallography at 2.37 A resolution. Moreover, from new data at 2.14 A resolution, the refined structure of the complex of TK with its substrate deoxythymidine (R = 0.209 for 96% of all data) now reveals much detail concerning substrate and solvent interactions with the enzyme. Structures of the complexes of TK with four halogen-containing substrate analogs have also been solved, to resolutions better than 2.4 A. The various TK inhibitors broadly fall into three groups which together probe the space of the enzyme active site in a manner that no one molecule does alone, so giving a composite picture of active site interactions that can be exploited in the design of novel compounds.
-Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.,Champness JN, Bennett MS, Wien F, Visse R, Summers WC, Herdewijn P, de Clerq E, Ostrowski T, Jarvest RL, Sanderson MR Proteins. 1998 Aug 15;32(3):350-61. PMID:9715911<ref>PMID:9715911</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ki4" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Thymidine kinase|Thymidine kinase]]
+*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Hhv-1]]
+[[Category: Human alphaherpesvirus 1 strain 17]]
-[[Category: Thymidine kinase]]
+[[Category: Large Structures]]
-[[Category: Bennett, M S]]
+[[Category: Bennett MS]]
-[[Category: Champness, J N]]
+[[Category: Champness JN]]
-[[Category: Sanderson, M R]]
+[[Category: Sanderson MR]]
-[[Category: Summers, W C]]
+[[Category: Summers WC]]
-[[Category: Visse, R]]
+[[Category: Visse R]]
-[[Category: Wien, F]]
+[[Category: Wien F]]
-[[Category: 5-bromothienyldeoxyuridine]]
-[[Category: Alphaherpesvirinae]]
-[[Category: Ds-dna enveloped viruse]]
-[[Category: Herpesviridae]]
-[[Category: Phosphotransferase]]
-[[Category: Substrate analog]]
-[[Category: Viridae]]