1vcd: Difference between revisions

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-[[Image:1vcd.png|left|200px]]
-{{STRUCTURE_1vcd|  PDB=1vcd  |  SCENE=  }}
+==Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1==
+<StructureSection load='1vcd' size='340' side='right'caption='[[1vcd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vcd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCD FirstGlance]. <br>
+</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1vcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcd OCA], [https://pdbe.org/1vcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcd RCSB], [https://www.ebi.ac.uk/pdbsum/1vcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcd ProSAT], [https://www.topsan.org/Proteins/RSGI/1vcd TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDX1_THETH NDX1_THETH] Specifically hydrolyzes (di)adenosine polyphosphates but not ATP or diadenosine triphosphate, generating ATP as the product. Diadenosine hexaphosphate (Ap6A) is the preferred substrate and its hydrolyzation yields 2 ATP. It is the only enzyme that symmetrically hydrolyzes Ap6A. It also hydrolyzes diadenosine pentaphosphate (Ap5A), diadenosine tetraphosphate (Ap4A), adenosine tetraphosphate (p4A) to produce ATP and ADP, ATP and AMP, ATP and inorganic orthophosphate, respectively.<ref>PMID:15024014</ref>
+== 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/vc/1vcd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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/main_output.php?pdb_ID=1vcd ConSurf].
+<div style="clear:both"></div>
-===Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1===
+==See Also==
+*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-[[1vcd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCD OCA].
+__TOC__
-[[Category: Thermus thermophilus hb8]]
+</StructureSection>
-[[Category: Iwai, T.]]
+[[Category: Large Structures]]
-[[Category: Kuramitsu, S.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Masui, R.]]
+[[Category: Iwai T]]
-[[Category: Nakagawa, N.]]
+[[Category: Kuramitsu S]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Masui R]]
-[[Category: Ap6a]]
+[[Category: Nakagawa N]]
-[[Category: Diadenosine polyphosphate]]
-[[Category: Hydrolase]]
-[[Category: Nudix protein]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Thermus thermophilus hb8]]