3nya: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3nya.png|left|200px]]
-<!--
+==Crystal structure of the human beta2 adrenergic receptor in complex with the neutral antagonist alprenolol==
-The line below this paragraph, containing "STRUCTURE_3nya", creates the "Structure Box" on the page.
+<StructureSection load='3nya' size='340' side='right'caption='[[3nya]], [[Resolution|resolution]] 3.16&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'>[[3nya]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] 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=3NYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYA 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]] 3.16&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=JTZ:(2S)-1-[(1-METHYLETHYL)AMINO]-3-(2-PROP-2-EN-1-YLPHENOXY)PROPAN-2-OL'>JTZ</scene></td></tr>
-{{STRUCTURE_3nya|  PDB=3nya  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nya OCA], [https://pdbe.org/3nya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nya RCSB], [https://www.ebi.ac.uk/pdbsum/3nya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nya ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADRB2_HUMAN ADRB2_HUMAN] Beta-adrenergic receptors mediate the catecholamine-induced activation of adenylate cyclase through the action of G proteins. The beta-2-adrenergic receptor binds epinephrine with an approximately 30-fold greater affinity than it does norepinephrine.[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</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/ny/3nya_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3nya ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+G protein-coupled receptors (GPCRs) represent a large fraction of current pharmaceutical targets, and of the GPCRs, the beta(2) adrenergic receptor (beta(2)AR) is one of the most extensively studied. Previously, the X-ray crystal structure of beta(2)AR has been determined in complex with two partial inverse agonists, but the global impact of additional ligands on the structure or local impacts on the binding site are not well-understood. To assess the extent of such ligand-induced conformational differences, we determined the crystal structures of a previously described engineered beta(2)AR construct in complex with two inverse agonists: ICI 118,551 (2.8 A), a recently described compound (2.8 A) (Kolb et al, 2009), and the antagonist alprenolol (3.1 A). The structures show the same overall fold observed for the previous beta(2)AR structures and demonstrate that the ligand binding site can accommodate compounds of different chemical and pharmacological properties with only minor local structural rearrangements. All three compounds contain a hydroxy-amine motif that establishes a conserved hydrogen bond network with the receptor and chemically diverse aromatic moieties that form distinct interactions with beta(2)AR. Furthermore, receptor ligand cross-docking experiments revealed that a single beta(2)AR complex can be suitable for docking of a range of antagonists and inverse agonists but also indicate that additional ligand-receptor structures may be useful to further improve performance for in-silico docking or lead-optimization in drug design.
-===Crystal structure of the human beta2 adrenergic receptor in complex with the neutral antagonist alprenolol===
+Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography.,Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, Stevens RC J Am Chem Soc. 2010 Aug 25;132(33):11443-5. PMID:20669948<ref>PMID:20669948</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20669948}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3nya" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20669948 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_20669948}}
-==About this Structure==
-[[3nya]] is a 1 chain structure of [[Adrenergic receptor]] and [[Hen Egg-White (HEW) Lysozyme]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens,_enterobacteria_phage_t4 Homo sapiens, enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYA OCA].
 ==See Also==
-*[[Adrenergic receptor|Adrenergic receptor]]
+*[[Adrenergic receptor 3D structures|Adrenergic receptor 3D structures]]
-*[[Hen Egg-White (HEW) Lysozyme|Hen Egg-White (HEW) Lysozyme]]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020669948</ref><references group="xtra"/>
+__TOC__
-[[Category: Homo sapiens, enterobacteria phage t4]]
+</StructureSection>
-[[Category: Abagyan, R.]]
+[[Category: Escherichia virus T4]]
-[[Category: Brown, M A.]]
+[[Category: Homo sapiens]]
-[[Category: Cherezov, V.]]
+[[Category: Large Structures]]
-[[Category: Fenalti, G.]]
+[[Category: Abagyan R]]
-[[Category: Katritch, V.]]
+[[Category: Brown MA]]
-[[Category: Stevens, R C.]]
+[[Category: Cherezov V]]
-[[Category: Wacker, D.]]
+[[Category: Fenalti G]]
-[[Category: Adrenaline]]
+[[Category: Katritch V]]
-[[Category: Adrenergic]]
+[[Category: Stevens RC]]
-[[Category: Alprenolol]]
+[[Category: Wacker D]]
-[[Category: Arrestin]]
-[[Category: Fusion]]
-[[Category: G protein-coupled receptor]]
-[[Category: G-protein]]
-[[Category: Glycosylation]]
-[[Category: Hydrolase]]
-[[Category: Lysozyme]]
-[[Category: Membrane protein]]
-[[Category: Palmitoylation]]
-[[Category: Phosphorylation]]
-[[Category: Transducer]]