2f64

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{{STRUCTURE_2f64| PDB=2f64 | SCENE= }}
 
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===Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-2(1H)-ONE bound===
 
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{{ABSTRACT_PUBMED_17004709}}
 
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==About this Structure==
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==Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-2(1H)-ONE bound==
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[[2f64]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F64 OCA].
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<StructureSection load='2f64' size='340' side='right'caption='[[2f64]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2f64]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F64 FirstGlance]. <br>
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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]] 1.6&#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=12Q:1-METHYLQUINOLIN-2(1H)-ONE'>12Q</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=2f64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f64 OCA], [https://pdbe.org/2f64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f64 RCSB], [https://www.ebi.ac.uk/pdbsum/2f64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f64 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q57VC7_TRYB2 Q57VC7_TRYB2]
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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/f6/2f64_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2f64 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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The 1.8 A resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SADa phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identify novel lead compounds, we exploited "fragment cocktail soaks". Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of approximately 10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.
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==Reference==
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Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.,Bosch J, Robien MA, Mehlin C, Boni E, Riechers A, Buckner FS, Van Voorhis WC, Myler PJ, Worthey EA, DeTitta G, Luft JR, Lauricella A, Gulde S, Anderson LA, Kalyuzhniy O, Neely HM, Ross J, Earnest TN, Soltis M, Schoenfeld L, Zucker F, Merritt EA, Fan E, Verlinde CL, Hol WG J Med Chem. 2006 Oct 5;49(20):5939-46. PMID:17004709<ref>PMID:17004709</ref>
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<ref group="xtra">PMID:017004709</ref><references group="xtra"/><references/>
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[[Category: Nucleoside deoxyribosyltransferase]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Trypanosoma brucei]]
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</div>
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[[Category: Bosch, J.]]
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<div class="pdbe-citations 2f64" style="background-color:#fffaf0;"></div>
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[[Category: Hol, W G.J.]]
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== References ==
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[[Category: Robien, M A.]]
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<references/>
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[[Category: SGPP, Structural Genomics of Pathogenic Protozoa Consortium.]]
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__TOC__
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[[Category: Nucleoside 2-deoxyribosyltransferase]]
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</StructureSection>
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[[Category: Protein structure initiative ndrt]]
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[[Category: Large Structures]]
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[[Category: Psi]]
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[[Category: Sgpp]]
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[[Category: Structural genomic]]
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[[Category: Structural genomics of pathogenic protozoa consortium]]
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[[Category: Transferase]]
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[[Category: Trypanosoma brucei]]
[[Category: Trypanosoma brucei]]
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[[Category: Bosch J]]
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[[Category: Hol WGJ]]
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[[Category: Robien MA]]

Current revision

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-2(1H)-ONE bound

PDB ID 2f64

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