3d1v

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{{Seed}}
 
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[[Image:3d1v.jpg|left|200px]]
 
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==Crystal structure of human PNP complexed with 2-mercapto(3H) quinazolinone==
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The line below this paragraph, containing "STRUCTURE_3d1v", creates the "Structure Box" on the page.
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<StructureSection load='3d1v' size='340' side='right'caption='[[3d1v]], [[Resolution|resolution]] 2.70&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'>[[3d1v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1V 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]] 2.7&#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=D1V:2-MERCAPTO(3H)QUINAZOLINONE'>D1V</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_3d1v| PDB=3d1v | 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=3d1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1v OCA], [https://pdbe.org/3d1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1v RCSB], [https://www.ebi.ac.uk/pdbsum/3d1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1v ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN] Defects in PNP are the cause of purine nucleoside phosphorylase deficiency (PNPD) [MIM:[https://omim.org/entry/613179 613179]. It leads to a severe T-cell immunodeficiency with neurologic disorder in children.<ref>PMID:3029074</ref> <ref>PMID:1384322</ref> <ref>PMID:8931706</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.<ref>PMID:2104852</ref>
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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/d1/3d1v_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=3d1v 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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Human purine nucleoside phosphorylase (HsPNP) is a target for inhibitor development aiming at T-cell immune response modulation. In this work, we report the development of a new set of empirical scoring functions and its application to evaluate binding affinities and docking results. To test these new functions, we solved the structure of HsPNP and 2-mercapto-4(3H)-quinazolinone (HsPNP:MQU) binary complex at 2.7A resolution using synchrotron radiation, and used these functions to predict ligand position obtained in docking simulations. We also employed molecular dynamics simulations to analyze HsPNP in two conditions, as apoenzyme and in the binary complex form, in order to assess the structural features responsible for stability. Analysis of the structural differences between systems provides explanation for inhibitor binding. The use of these scoring functions to evaluate binding affinities and molecular docking results may be used to guide future efforts on virtual screening focused on HsPNP.
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===Crystal structure of human PNP complexed with 2-mercapto(3H) quinazolinone===
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Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function.,Timmers LF, Caceres RA, Vivan AL, Gava LM, Dias R, Ducati RG, Basso LA, Santos DS, de Azevedo WF Jr Arch Biochem Biophys. 2008 Nov 1;479(1):28-38. Epub 2008 Aug 30. PMID:18790691<ref>PMID:18790691</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>
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<div class="pdbe-citations 3d1v" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18790691}}, adds the Publication Abstract to the page
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*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18790691 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18790691}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3D1V is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1V OCA].
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==Reference==
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<ref group="xtra">PMID:18790691</ref><ref group="xtra">PMID:12914785</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Purine-nucleoside phosphorylase]]
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[[Category: Large Structures]]
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[[Category: Basso, L A.]]
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[[Category: Basso LA]]
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[[Category: Jr., W F.De Azevedo.]]
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[[Category: De Azevedo Jr WF]]
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[[Category: Santos, D S.]]
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[[Category: Santos DS]]
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[[Category: Acetylation]]
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[[Category: Crystallography]]
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[[Category: Disease mutation]]
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[[Category: Drug design]]
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[[Category: Empirical scoring function]]
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[[Category: Glycosyltransferase]]
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[[Category: Polymorphism]]
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[[Category: Purine nucleoside phosphorylase]]
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[[Category: Synchrotron]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 15 08:46:16 2009''
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Current revision

Crystal structure of human PNP complexed with 2-mercapto(3H) quinazolinone

PDB ID 3d1v

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