1xot: Difference between revisions

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-{{Seed}}
-[[Image:1xot.png|left|200px]]
-<!--
+==Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Vardenafil==
-The line below this paragraph, containing "STRUCTURE_1xot", creates the "Structure Box" on the page.
+<StructureSection load='1xot' size='340' side='right'caption='[[1xot]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1xot]] is a 2 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=1XOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XOT FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.34&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VDN:2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE'>VDN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1xot|  PDB=1xot  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xot OCA], [https://pdbe.org/1xot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xot RCSB], [https://www.ebi.ac.uk/pdbsum/1xot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xot ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDE4B_HUMAN PDE4B_HUMAN] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents.<ref>PMID:10846163</ref> <ref>PMID:15003452</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xo/1xot_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1xot ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phosphodiesterases (PDEs) comprise a large family of enzymes that catalyze the hydrolysis of cAMP or cGMP and are implicated in various diseases. We describe the high-resolution crystal structures of the catalytic domains of PDE4B, PDE4D, and PDE5A with ten different inhibitors, including the drug candidates cilomilast and roflumilast, for respiratory diseases. These cocrystal structures reveal a common scheme of inhibitor binding to the PDEs: (i) a hydrophobic clamp formed by highly conserved hydrophobic residues that sandwich the inhibitor in the active site; (ii) hydrogen bonding to an invariant glutamine that controls the orientation of inhibitor binding. A scaffold can be readily identified for any given inhibitor based on the formation of these two types of conserved interactions. These structural insights will enable the design of isoform-selective inhibitors with improved binding affinity and should facilitate the discovery of more potent and selective PDE inhibitors for the treatment of a variety of diseases.
-===Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Vardenafil===
+Structural basis for the activity of drugs that inhibit phosphodiesterases.,Card GL, England BP, Suzuki Y, Fong D, Powell B, Lee B, Luu C, Tabrizizad M, Gillette S, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY Structure. 2004 Dec;12(12):2233-47. PMID:15576036<ref>PMID:15576036</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1xot" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15576036}}, adds the Publication Abstract to the page
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15576036 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15576036}}
+__TOC__
+</StructureSection>
-==About this Structure==
-XOT is a [[Single protein]] 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=1XOT OCA].
-==Reference==
-Structural basis for the activity of drugs that inhibit phosphodiesterases., Card GL, England BP, Suzuki Y, Fong D, Powell B, Lee B, Luu C, Tabrizizad M, Gillette S, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY, Structure. 2004 Dec;12(12):2233-47. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15576036 15576036]
-[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Artis, D R.]]
+[[Category: Artis DR]]
-[[Category: Bollag, G.]]
+[[Category: Bollag G]]
-[[Category: Card, G L.]]
+[[Category: Card GL]]
-[[Category: England, B P.]]
+[[Category: England BP]]
-[[Category: Fong, D.]]
+[[Category: Fong D]]
-[[Category: Gillette, S.]]
+[[Category: Gillette S]]
-[[Category: Ibrahim, P N.]]
+[[Category: Ibrahim PN]]
-[[Category: Kim, S H.]]
+[[Category: Kim S-H]]
-[[Category: Lee, B.]]
+[[Category: Lee B]]
-[[Category: Luu, C.]]
+[[Category: Luu C]]
-[[Category: Milburn, M V.]]
+[[Category: Milburn MV]]
-[[Category: Powell, B.]]
+[[Category: Powell B]]
-[[Category: Schlessinger, J.]]
+[[Category: Schlessinger J]]
-[[Category: Suzuki, Y.]]
+[[Category: Suzuki Y]]
-[[Category: Tabrizizad, M.]]
+[[Category: Tabrizizad M]]
-[[Category: Zhang, K Y.J.]]
+[[Category: Zhang KYJ]]
-[[Category: Levitra]]
-[[Category: Pde]]
-[[Category: Pde4b]]
-[[Category: Phosphodiesterase]]
-[[Category: Vardenafil]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 08:45:01 2008''