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1rkp

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(New page: 200px<br /> <applet load="1rkp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rkp, resolution 2.05&Aring;" /> '''Crystal structure o...)
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[[Image:1rkp.gif|left|200px]]<br />
 
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<applet load="1rkp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rkp, resolution 2.05&Aring;" />
 
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'''Crystal structure of PDE5A1-IBMX'''<br />
 
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==Overview==
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==Crystal structure of PDE5A1-IBMX==
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Cyclic nucleotide phosphodiesterases (PDEs) are a superfamily of enzymes, controlling cellular concentrations of the second messengers cAMP and, cGMP. Crystal structures of the catalytic domains of cGMP-specific PDE5A1, and cAMP-specific PDE4D2 in complex with the nonselective inhibitor, 3-isobutyl-1-methylxanthine have been determined at medium resolution. The, catalytic domain of PDE5A1 has the same topological folding as that of, PDE4D2, but three regions show different tertiary structures, including, residues 79-113, 208-224 (H-loop), and 341-364 (M-loop) in PDE4D2 or, 535-566, 661-676, and 787-812 in PDE5A1, respectively. Because H- and, M-loops are involved in binding of the selective inhibitors, the different, conformations of the loops, thus the distinct shapes of the active sites, will be a determinant of inhibitor selectivity in PDEs. IBMX binds to a, subpocket that comprises key residues Ile-336, Phe-340, Gln-369, and, Phe-372 of PDE4D2 or Val-782, Phe-786, Gln-817, and Phe-820 of PDE5A1., This subpocket may be a common site for binding nonselective inhibitors of, PDEs.
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<StructureSection load='1rkp' size='340' side='right'caption='[[1rkp]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rkp]] 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=1RKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKP 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]] 2.05&#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=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1rkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkp OCA], [https://pdbe.org/1rkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkp RCSB], [https://www.ebi.ac.uk/pdbsum/1rkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PDE5A_HUMAN PDE5A_HUMAN] Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This phosphodiesterase catalyzes the specific hydrolysis of cGMP to 5'-GMP.
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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/rk/1rkp_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=1rkp ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RKP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN, MG and IBM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RKP OCA].
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*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structures of phosphodiesterases 4 and 5 in complex with inhibitor 3-isobutyl-1-methylxanthine suggest a conformation determinant of inhibitor selectivity., Huai Q, Liu Y, Francis SH, Corbin JD, Ke H, J Biol Chem. 2004 Mar 26;279(13):13095-101. Epub 2003 Dec 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14668322 14668322]
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[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Corbin, J.D.]]
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[[Category: Corbin JD]]
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[[Category: Francis, S.H.]]
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[[Category: Francis SH]]
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[[Category: Huai, Q.]]
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[[Category: Huai Q]]
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[[Category: Ke, H.]]
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[[Category: Ke H]]
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[[Category: Liu, Y.]]
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[[Category: Liu Y]]
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[[Category: IBM]]
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[[Category: MG]]
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[[Category: ZN]]
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[[Category: ibmx]]
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[[Category: pde5a]]
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[[Category: viagra]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 19:05:10 2007''
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Current revision

Crystal structure of PDE5A1-IBMX

PDB ID 1rkp

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