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3epw

From Proteopedia

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(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_3epw", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
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[[Image:3epw.png|left|200px]]
 
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==Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidin-3,4-diol==
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The line below this paragraph, containing "STRUCTURE_3epw", creates the "Structure Box" on the page.
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<StructureSection load='3epw' size='340' side='right'caption='[[3epw]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3epw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_vivax Trypanosoma vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPW FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=JMQ:7-(((2R,3R,4S)-3,4-DIHYDROXY-2-(HYDROXYMETHYL)PYRROLIDIN-1-YL)METHYL)-3H-PYRROLO[3,2-D]PYRIMIDIN-4(5H)-ONE'>JMQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_3epw| PDB=3epw | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3epw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epw OCA], [https://pdbe.org/3epw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3epw RCSB], [https://www.ebi.ac.uk/pdbsum/3epw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3epw ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9GPQ4_TRYVI Q9GPQ4_TRYVI]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3epw_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3epw ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Diseases caused by parasitic protozoa remain a major health problem, mainly due to old toxic drugs and rising drug resistance. Nucleoside hydrolases are key enzymes of the purine salvage pathway of parasites from the Trypanosomatidae family and are considered as possible drug targets. N-Arylmethyl substituted iminoribitols have been developed as selective nanomolar affinity inhibitors against the purine-specific nucleoside hydrolase of Trypanosoma vivax. The current paper describes the crystal structures of the T. vivax nucleoside hydrolase in complex with two of these inhibitors, to 1.3 and 1.85 A resolution. These high resolution structures provide an accurate picture of the mode of binding of these inhibitors and their mechanism of transition-state mimicry, and are valuable tools to guide further inhibitor design. Comparison of the current structures with previously solved structures of the enzyme in complex with ground-state and transition-state-analogue inhibitors also allows for the elucidation of a detailed molecular mechanism of active-site loop opening/closing. These loop movements can be coupled to the complex kinetic mechanism of the T. vivax nucleoside hydrolase.
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===Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidin-3,4-diol===
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Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors.,Versees W, Goeminne A, Berg M, Vandemeulebroucke A, Haemers A, Augustyns K, Steyaert J Biochim Biophys Acta. 2009 Jun;1794(6):953-60. Epub 2009 Mar 10. PMID:19281874<ref>PMID:19281874</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3epw" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19281874 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19281874}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[3epw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_vivax Trypanosoma vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPW OCA].
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==Reference==
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<ref group="xtra">PMID:019281874</ref><references group="xtra"/>
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[[Category: Purine nucleosidase]]
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[[Category: Trypanosoma vivax]]
[[Category: Trypanosoma vivax]]
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[[Category: Augustyns, K]]
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[[Category: Augustyns K]]
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[[Category: Berg, M.]]
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[[Category: Berg M]]
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[[Category: Goeminne, A.]]
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[[Category: Goeminne A]]
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[[Category: Haemers, A.]]
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[[Category: Haemers A]]
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[[Category: Steyaert, J.]]
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[[Category: Steyaert J]]
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[[Category: Vandemeulebroucke, A.]]
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[[Category: Vandemeulebroucke A]]
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[[Category: Versees, W.]]
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[[Category: Versees W]]
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[[Category: Active site loop]]
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[[Category: Aromatic stacking]]
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[[Category: Hydrolase]]
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[[Category: Rossmann fold]]
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Current revision

Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidin-3,4-diol

PDB ID 3epw

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