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6ay1 - Revision history
2026-04-12T22:32:15Z
Revision history for this page on the wiki
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OCA at 14:28, 4 October 2023
2023-10-04T14:28:22Z
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<td colspan='2' style="background-color: white; color:black;">←Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 14:28, 4 October 2023</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><StructureSection load='6ay1' size='340' side='right' caption='[[6ay1]], [[Resolution|resolution]] 2.05&Aring;' scene=''></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><StructureSection load='6ay1' size='340' side='right'caption='[[6ay1]], [[Resolution|resolution]] 2.05&Aring;' scene=''></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Structural highlights ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Structural highlights ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><table><tr><td colspan='2'>[[6ay1]] is a 8 chain structure with sequence from [<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://en.wikipedia.org/wiki/<del style="color: red; font-weight: bold; text-decoration: none;">Atcc_43504 Atcc 43504</del>]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AY1 OCA]. For a <b>guided tour on the structure components</b> use [<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://<del style="color: red; font-weight: bold; text-decoration: none;">oca</del>.<del style="color: red; font-weight: bold; text-decoration: none;">weizmann.ac.il/oca-docs</del>/fgij/fg.htm?mol=6AY1 FirstGlance]. <br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><table><tr><td colspan='2'>[[6ay1]] is a 8 chain structure with sequence from [<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://en.wikipedia.org/wiki/<ins style="color: red; font-weight: bold; text-decoration: none;">Helicobacter_pylori Helicobacter pylori</ins>]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AY1 OCA]. For a <b>guided tour on the structure components</b> use [<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://<ins style="color: red; font-weight: bold; text-decoration: none;">proteopedia</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">org</ins>/fgij/fg.htm?mol=6AY1 FirstGlance]. <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div></td></tr><tr id='<del style="color: red; font-weight: bold; text-decoration: none;">ligand</del>'><td class="sblockLbl"><b>[[<del style="color: red; font-weight: bold; text-decoration: none;">Ligand</del>|<del style="color: red; font-weight: bold; text-decoration: none;">Ligands</del>:]]</b></td><td class="sblockDat"><del style="color: red; font-weight: bold; text-decoration: none;"><scene name='pdbligand=HEZ:HEXANE</del>-<del style="color: red; font-weight: bold; text-decoration: none;">1</del>,<del style="color: red; font-weight: bold; text-decoration: none;">6-DIOL'>HEZ</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MPD:(4S)-</del>2<del style="color: red; font-weight: bold; text-decoration: none;">-METHYL-2,4-PENTANEDIOL'>MPD</scene></del></td></tr></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></td></tr><tr id='<ins style="color: red; font-weight: bold; text-decoration: none;">method</ins>'><td class="sblockLbl"><b>[[<ins style="color: red; font-weight: bold; text-decoration: none;">Empirical_models</ins>|<ins style="color: red; font-weight: bold; text-decoration: none;">Method</ins>:]]</b></td><td class="sblockDat<ins style="color: red; font-weight: bold; text-decoration: none;">" id="methodDat</ins>"><ins style="color: red; font-weight: bold; text-decoration: none;">X</ins>-<ins style="color: red; font-weight: bold; text-decoration: none;">ray diffraction</ins>, <ins style="color: red; font-weight: bold; text-decoration: none;">[[Resolution|Resolution]] </ins>2<ins style="color: red; font-weight: bold; text-decoration: none;">.05&#8491;</ins></td></tr></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><tr id='<del style="color: red; font-weight: bold; text-decoration: none;">gene</del>'><td class="sblockLbl"><b>[[<del style="color: red; font-weight: bold; text-decoration: none;">Gene</del>|<del style="color: red; font-weight: bold; text-decoration: none;">Gene</del>:]]</b></td><td class="sblockDat"><del style="color: red; font-weight: bold; text-decoration: none;">ndk, HPG27_182 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode</del>=<del style="color: red; font-weight: bold; text-decoration: none;">Info&srchmode</del>=<del style="color: red; font-weight: bold; text-decoration: none;">5&id=210 ATCC 43504])</td</del>></<del style="color: red; font-weight: bold; text-decoration: none;">tr</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><tr id='<ins style="color: red; font-weight: bold; text-decoration: none;">ligand</ins>'><td class="sblockLbl"><b>[[<ins style="color: red; font-weight: bold; text-decoration: none;">Ligand</ins>|<ins style="color: red; font-weight: bold; text-decoration: none;">Ligands</ins>:]]</b></td><td class="sblockDat<ins style="color: red; font-weight: bold; text-decoration: none;">" id="ligandDat</ins>"><ins style="color: red; font-weight: bold; text-decoration: none;"><scene name</ins>=<ins style="color: red; font-weight: bold; text-decoration: none;">'pdbligand</ins>=<ins style="color: red; font-weight: bold; text-decoration: none;">HEZ:HEXANE-1,6-DIOL'</ins>><ins style="color: red; font-weight: bold; text-decoration: none;">HEZ</ins></<ins style="color: red; font-weight: bold; text-decoration: none;">scene</ins>><ins style="color: red; font-weight: bold; text-decoration: none;">, </ins><<ins style="color: red; font-weight: bold; text-decoration: none;">scene name</ins>='<ins style="color: red; font-weight: bold; text-decoration: none;">pdbligand</ins>=<ins style="color: red; font-weight: bold; text-decoration: none;">IPA</ins>:<ins style="color: red; font-weight: bold; text-decoration: none;">ISOPROPYL+ALCOHOL'</ins>><ins style="color: red; font-weight: bold; text-decoration: none;">IPA</ins></<ins style="color: red; font-weight: bold; text-decoration: none;">scene</ins>><ins style="color: red; font-weight: bold; text-decoration: none;">, </ins><<ins style="color: red; font-weight: bold; text-decoration: none;">scene name</ins>=<ins style="color: red; font-weight: bold; text-decoration: none;">'pdbligand</ins>=<ins style="color: red; font-weight: bold; text-decoration: none;">MPD</ins>:<ins style="color: red; font-weight: bold; text-decoration: none;">(4S)</ins>-<ins style="color: red; font-weight: bold; text-decoration: none;">2</ins>-<ins style="color: red; font-weight: bold; text-decoration: none;">METHYL</ins>-2<ins style="color: red; font-weight: bold; text-decoration: none;">,</ins>4<ins style="color: red; font-weight: bold; text-decoration: none;">-PENTANEDIOL'>MPD</ins></<ins style="color: red; font-weight: bold; text-decoration: none;">scene</ins>></td></tr></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><<del style="color: red; font-weight: bold; text-decoration: none;">tr id</del>='<del style="color: red; font-weight: bold; text-decoration: none;">activity'><td class</del>=<del style="color: red; font-weight: bold; text-decoration: none;">"sblockLbl"><b>Activity</del>:<del style="color: red; font-weight: bold; text-decoration: none;"></b</del>></<del style="color: red; font-weight: bold; text-decoration: none;">td</del>><<del style="color: red; font-weight: bold; text-decoration: none;">td class</del>=<del style="color: red; font-weight: bold; text-decoration: none;">"sblockDat"><span class</del>=<del style="color: red; font-weight: bold; text-decoration: none;">'plainlinks'>[http</del>:<del style="color: red; font-weight: bold; text-decoration: none;">//en.wikipedia.org/wiki/Nucleoside</del>-<del style="color: red; font-weight: bold; text-decoration: none;">diphosphate_kinase Nucleoside</del>-<del style="color: red; font-weight: bold; text-decoration: none;">diphosphate kinase], with EC number [http://www.brenda</del>-<del style="color: red; font-weight: bold; text-decoration: none;">enzymes.info/php/result_flat.php4?ecno=</del>2<del style="color: red; font-weight: bold; text-decoration: none;">.7.</del>4<del style="color: red; font-weight: bold; text-decoration: none;">.6 2.7.4.6] </del></<del style="color: red; font-weight: bold; text-decoration: none;">span</del>></td></tr></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://<ins style="color: red; font-weight: bold; text-decoration: none;">proteopedia</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">org</ins>/fgij/fg.htm?mol=6ay1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ay1 OCA], [<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://pdbe.org/6ay1 PDBe], [<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://www.rcsb.org/pdb/explore.do?structureId=6ay1 RCSB], [<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://www.ebi.ac.uk/pdbsum/6ay1 PDBsum], [<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://prosat.h-its.org/prosat/prosatexe?pdbcode=6ay1 ProSAT]</span></td></tr></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://<del style="color: red; font-weight: bold; text-decoration: none;">oca</del>.<del style="color: red; font-weight: bold; text-decoration: none;">weizmann.ac.il/oca-docs</del>/fgij/fg.htm?mol=6ay1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ay1 OCA], [<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://pdbe.org/6ay1 PDBe], [<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://www.rcsb.org/pdb/explore.do?structureId=6ay1 RCSB], [<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://www.ebi.ac.uk/pdbsum/6ay1 PDBsum], [<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://prosat.h-its.org/prosat/prosatexe?pdbcode=6ay1 ProSAT]</span></td></tr></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></table></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Function ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Function ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[<del style="color: red; font-weight: bold; text-decoration: none;">[http</del>://www.uniprot.org/uniprot/NDK_HELPG NDK_HELPG<del style="color: red; font-weight: bold; text-decoration: none;">]</del>] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://www.uniprot.org/uniprot/NDK_HELPG NDK_HELPG] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==See Also==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__TOC__</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__TOC__</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></StructureSection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></StructureSection></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Category: <del style="color: red; font-weight: bold; text-decoration: none;">Atcc 43504</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Category: <ins style="color: red; font-weight: bold; text-decoration: none;">Helicobacter pylori</ins>]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Category: <del style="color: red; font-weight: bold; text-decoration: none;">Nucleoside-diphosphate kinase</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Category: <ins style="color: red; font-weight: bold; text-decoration: none;">Large Structures</ins>]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Category: Edwards<del style="color: red; font-weight: bold; text-decoration: none;">, T E]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Category: Edwards <ins style="color: red; font-weight: bold; text-decoration: none;">TE</ins>]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Structural genomic]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Atp-dependent]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Kinase]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Ndk]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Ndpk]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Niaid]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Ssgcid]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category: Transferase</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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OCA
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OCA: Protected "6ay1" [edit=sysop:move=sysop]
2017-11-15T14:37:08Z
<p>Protected "<a href="/wiki/index.php/6ay1" title="6ay1">6ay1</a>" [edit=sysop:move=sysop]</p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 14:37, 15 November 2017</td>
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OCA
http://52.214.119.220/wiki/index.php?title=6ay1&diff=2813219&oldid=prev
OCA: New page: ==Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori== <StructureSection load='6ay1' size='340' side='right' caption='6ay1, resolution 2....
2017-11-15T14:37:06Z
<p>New page: ==Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori== <StructureSection load='6ay1' size='340' side='right' caption='<a href="/wiki/index.php/6ay1" title="6ay1">6ay1</a>, <a href="/wiki/index.php/Resolution" title="Resolution">resolution</a> 2....</p>
<p><b>New page</b></p><div><br />
==Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori==<br />
<StructureSection load='6ay1' size='340' side='right' caption='[[6ay1]], [[Resolution|resolution]] 2.05&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[6ay1]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AY1 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr><br />
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndk, HPG27_182 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr><br />
<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><br />
<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=6ay1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ay1 OCA], [http://pdbe.org/6ay1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ay1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ay1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ay1 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[http://www.uniprot.org/uniprot/NDK_HELPG NDK_HELPG]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. <br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 43504]]<br />
[[Category: Nucleoside-diphosphate kinase]]<br />
[[Category: Edwards, T E]]<br />
[[Category: Structural genomic]]<br />
[[Category: Atp-dependent]]<br />
[[Category: Kinase]]<br />
[[Category: Ndk]]<br />
[[Category: Ndpk]]<br />
[[Category: Niaid]]<br />
[[Category: Ssgcid]]<br />
[[Category: Transferase]]</div>
OCA