1yp7: Difference between revisions

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-{{Seed}}
-[[Image:1yp7.png|left|200px]]
-<!--
+==Van der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site Occluded From Solvent Water==
-The line below this paragraph, containing "STRUCTURE_1yp7", creates the "Structure Box" on the page.
+<StructureSection load='1yp7' size='340' side='right'caption='[[1yp7]], [[Resolution|resolution]] 2.00&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'>[[1yp7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YP7 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-{{STRUCTURE_1yp7|  PDB=1yp7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yp7 OCA], [https://pdbe.org/1yp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yp7 RCSB], [https://www.ebi.ac.uk/pdbsum/1yp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yp7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MUP1_MOUSE MUP1_MOUSE] Binds pheromones that are released from drying urine of males. These pheromones affect the sexual behavior of females.
+== 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/yp/1yp7_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=1yp7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the present study we examine the enthalpy of binding of 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and site-directed mutagenesis. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected given that the binding pocket of MUP-1 is very hydrophobic. The only ligand-protein hydrogen bond is formed between the side-chain hydroxyl of Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC measurements on the binding of IBMP to the Y120F mutant demonstrate a reduced enthalpy of binding, but nonetheless binding is still enthalpy dominated. A combination of solvent isotopic substitution ITC measurements and all-atom molecular dynamics simulations with explicit inclusion of solvent water suggests that solvation is not a major contributor to the overall binding enthalpy. Moreover, hydrogen/deuterium exchange measurements suggest that there is no significant contribution to the enthalpy of binding derived from "tightening" of the protein structure. Data are consistent with binding thermodynamics dominated by favorable dispersion interactions, arising from the inequality of solvent-solute dispersion interactions before complexation versus solute-solute dispersion interactions after complexation, by virtue of poor solvation of the binding pocket.
-===Van der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site Occluded From Solvent Water===
+Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water.,Barratt E, Bingham RJ, Warner DJ, Laughton CA, Phillips SE, Homans SW J Am Chem Soc. 2005 Aug 24;127(33):11827-34. PMID:16104761<ref>PMID:16104761</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_16104761}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1yp7" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16104761 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16104761}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-YP7 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YP7 OCA].
-==Reference==
-<ref group="xtra">PMID:16104761</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Barratt, E.]]
+[[Category: Barratt E]]
-[[Category: Bingham, R J.]]
+[[Category: Bingham RJ]]
-[[Category: Homans, S W.]]
+[[Category: Homans SW]]
-[[Category: Laughton, C A.]]
+[[Category: Laughton CA]]
-[[Category: Phillips, S E.V.]]
+[[Category: Phillips SEV]]
-[[Category: Warner, D J.]]
+[[Category: Warner DJ]]
-[[Category: 2-methoxy-3-isobutylpyrazine]]
-[[Category: Beta-barrel]]
-[[Category: Lipocalin]]
-[[Category: Mup1]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:42:16 2009''