2hbh: Difference between revisions

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-[[Image:2hbh.png|left|200px]]
-{{STRUCTURE_2hbh|  PDB=2hbh  |  SCENE=  }}
+==Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide==
+<StructureSection load='2hbh' size='340' side='right'caption='[[2hbh]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2hbh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HBH FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XE4:1,3-CYCLOHEXANEDIOL,+4-METHYLENE-5-[(2E)-[(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL-1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]-,+(1R,3S,5Z)'>XE4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbh OCA], [https://pdbe.org/2hbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hbh RCSB], [https://www.ebi.ac.uk/pdbsum/2hbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</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/hb/2hbh_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=2hbh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.
-===Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide===
+Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol.,Rochel N, Hourai S, Perez-Garcia X, Rumbo A, Mourino A, Moras D Arch Biochem Biophys. 2007 Apr 15;460(2):172-6. Epub 2007 Feb 20. PMID:17346665<ref>PMID:17346665</ref>
-{{ABSTRACT_PUBMED_17346665}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2hbh" style="background-color:#fffaf0;"></div>
-[[2hbh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBH OCA].
 ==See Also==
-*[[Vitamin D receptor|Vitamin D receptor]]
+*[[Sandbox vdr|Sandbox vdr]]
+*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:017346665</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Danio rerio]]
-[[Category: Hourai, S.]]
+[[Category: Homo sapiens]]
-[[Category: Moras, D.]]
+[[Category: Large Structures]]
-[[Category: Rochel, N.]]
+[[Category: Hourai S]]
-[[Category: Alpha helical sandwich]]
+[[Category: Moras D]]
-[[Category: Gene regulation]]
+[[Category: Rochel N]]