1mn9: Difference between revisions

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<StructureSection load='1mn9' size='340' side='right'caption='[[1mn9]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='1mn9' size='340' side='right'caption='[[1mn9]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1mn9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dicdi Dicdi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MN9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1mn9]] 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=1MN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MN9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RTP:RIBAVIRIN+TRIPHOSPHATE'>RTP</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]] 2.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f3f|1f3f]], [[1nue|1nue]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RTP:RIBAVIRIN+TRIPHOSPHATE'>RTP</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1mn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mn9 OCA], [https://pdbe.org/1mn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mn9 RCSB], [https://www.ebi.ac.uk/pdbsum/1mn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mn9 ProSAT]</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=1mn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mn9 OCA], [https://pdbe.org/1mn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mn9 RCSB], [https://www.ebi.ac.uk/pdbsum/1mn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mn9 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1mn9 ConSurf].
</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=1mn9 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribavirin used in therapies against hepatitis C virus (HCV) is potentially efficient against other viruses but presents a high cytotoxicity. Several ribavirin triphosphate analogs modified on the ribose moiety were synthesized and tested in vitro on the RNA polymerases of HCV, phage T7, and HIV-1 reverse transcriptase. Modified nucleotides with 2'-deoxy, 3'-deoxy, 2',3'-dideoxy, 2',3'-dideoxy-2',3'-dehydro, and 2',3'-epoxy-ribose inhibited the HCV enzyme but not the other two polymerases. They were also analyzed as substrates for nucleoside diphosphate (NDP) kinase, the enzyme responsible for the last step of the cellular activation of antiviral nucleoside analogs. An X-ray structure of NDP kinase complexed with ribavirin triphosphate was determined. It demonstrates that the analog binds as a normal substrate despite the modified base and confirms the crucial role of the 3'-hydroxyl group in the phosphorylation reaction. The 3'-hydroxyl is required for inhibition of the initiation step of RNA synthesis by HCV polymerase, and both sugar hydroxyls must be present to inhibit elongation. The 2'deoxyribavirin is the only derivative efficient in vitro against HCV polymerase and properly activated by NDP kinase.
Structural analysis of the activation of ribavirin analogs by NDP kinase: comparison with other ribavirin targets.,Gallois-Montbrun S, Chen Y, Dutartre H, Sophys M, Morera S, Guerreiro C, Schneider B, Mulard L, Janin J, Veron M, Deville-Bonne D, Canard B Mol Pharmacol. 2003 Mar;63(3):538-46. PMID:12606760<ref>PMID:12606760</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1mn9" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dicdi]]
[[Category: Dictyostelium discoideum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Nucleoside-diphosphate kinase]]
[[Category: Canard B]]
[[Category: Canard, B]]
[[Category: Chen Y]]
[[Category: Chen, Y]]
[[Category: Deville-bonne D]]
[[Category: Deville-bonne, D]]
[[Category: Dutartre H]]
[[Category: Dutartre, H]]
[[Category: Gallois-montbrun S]]
[[Category: Gallois-montbrun, S]]
[[Category: Guerreiro C]]
[[Category: Guerreiro, C]]
[[Category: Janin J]]
[[Category: Janin, J]]
[[Category: Morera S]]
[[Category: Morera, S]]
[[Category: Mulard L]]
[[Category: Mulard, L]]
[[Category: Schneider B]]
[[Category: Schneider, B]]
[[Category: Veron M]]
[[Category: Veron, M]]
[[Category: Ndp kinase-ribavirin complex]]
[[Category: Transferase]]

Revision as of 11:38, 10 April 2024

NDP kinase mutant (H122G) complex with RTPNDP kinase mutant (H122G) complex with RTP

Structural highlights

1mn9 is a 3 chain structure with sequence from Dictyostelium discoideum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NDKC_DICDI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1mn9, resolution 2.90Å

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