2y54: Difference between revisions

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-[[Image:2y54.png|left|200px]]
-{{STRUCTURE_2y54|  PDB=2y54  |  SCENE=  }}
+==Fragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Fragment 1)==
+<StructureSection load='2y54' size='340' side='right'caption='[[2y54]], [[Resolution|resolution]] 3.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2y54]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Aplysia_californica Aplysia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y54 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]] 3.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=V63:[(1R,5S)-8-AZABICYCLO[3.2.1]OCTAN-3-YL]+BENZOATE'>V63</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=2y54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y54 OCA], [https://pdbe.org/2y54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y54 RCSB], [https://www.ebi.ac.uk/pdbsum/2y54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y54 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8WSF8_APLCA Q8WSF8_APLCA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding site of acetylcholine-binding protein (AChBP). This protein is a soluble homologue of the ligand binding domain (LBD) of Cys-loop receptors. The fragment optimization was monitored with X-ray structures of ligand complexes and systematic thermodynamic analyses using surface plasmon resonance (SPR) biosensor analysis and isothermal titration calorimetry (ITC). Using site-directed mutagenesis and AChBP from different species, we find that specific changes in thermodynamic binding profiles, are indicative of interactions with the ligand-inducible subpocket of AChBP. This study illustrates that thermodynamic analysis provides valuable information on ligand binding modes and is complementary to affinity data when guiding rational structure- and fragment-based discovery approaches.
-===FRAGMENT GROWING INDUCES CONFORMATIONAL CHANGES IN ACETYLCHOLINE-BINDING PROTEIN: A STRUCTURAL AND THERMODYNAMIC ANALYSIS - (FRAGMENT 1)===
+Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis.,Edink E, Rucktooa P, Retra K, Akdemir A, Nahar T, Zuiderveld O, van Elk R, Janssen E, van Nierop P, van Muijlwijk-Koezen J, Smit AB, Sixma TK, Leurs R, de Esch IJ J Am Chem Soc. 2011 Apr 13;133(14):5363-71. Epub 2011 Feb 15. PMID:21322593<ref>PMID:21322593</ref>
-{{ABSTRACT_PUBMED_21322593}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2y54" style="background-color:#fffaf0;"></div>
-[[2y54]] is a 5 chain structure of [[Acetylcholine binding protein]] with sequence from [http://en.wikipedia.org/wiki/Aplysia_californica Aplysia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y54 OCA].
 ==See Also==
-*[[Acetylcholine binding protein|Acetylcholine binding protein]]
+*[[Acetylcholine binding protein 3D structures|Acetylcholine binding protein 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:021322593</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Aplysia californica]]
-[[Category: Deesch, I J.P.]]
+[[Category: Large Structures]]
-[[Category: Edink, E.]]
+[[Category: Edink E]]
-[[Category: Rucktooa, P.]]
+[[Category: Rucktooa P]]
-[[Category: Sixma, T K.]]
+[[Category: Sixma TK]]
-[[Category: Receptor]]
+[[Category: DeEsch IJP]]