1bjv: Difference between revisions

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-[[Image:1bjv.png|left|200px]]
-{{STRUCTURE_1bjv|  PDB=1bjv  |  SCENE=  }}
+==BETA-TRYPSIN COMPLEXED WITH APPU==
+<StructureSection load='1bjv' size='340' side='right'caption='[[1bjv]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1bjv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BJV 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GP8:1-(2-AMIDINOPHENYL)-3-(PHENOXYPHENYL)UREA'>GP8</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1bjv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bjv OCA], [https://pdbe.org/1bjv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bjv RCSB], [https://www.ebi.ac.uk/pdbsum/1bjv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bjv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
+== 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/bj/1bjv_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=1bjv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Novel aryl derivatives of benzamidine were synthesized and tested for their inhibitory potency against bovine trypsin, rat skin tryptase, human recombinant granzyme A, human thrombin, and human plasma kallikrein. All compounds show competitive inhibition against these proteases with Ki values in the micromolar range. X-ray structures were determined to 1.8 A resolution for trypsin complexed with two of the para-substituted benzamidine derivatives, 1-(4-amidinophenyl)-3-(4-chlorophenyl)urea (ACPU) and 1-(4-amidinophenyl)-3-(4-phenoxyphenyl)urea (APPU). Although the inhibitors do not engage in direct and specific interactions outside the S1 pocket, they do form intimate indirect contacts with the active site of trypsin. The inhibitors are linked to the enzyme by a sulfate ion that forms an intricate network of three-centered hydrogen bonds. Comparison of these structures with other serine protease structures with noncovalently bound oxyanions reveals a pair of highly conserved oxyanion-binding sites in the active site. The positions of noncovalently bound oxyanions, such as the oxygen atoms of sulfate, are distinct from the positions of covalent oxyanions of tetrahedral intermediates. Noncovalent oxyanion positions are outside the "oxyanion hole." Kinetics data suggest that protonation stabilizes the ternary inhibitor/oxyanion/protease complex. In sum, both cations and anions can mediate Ki. Cation mediation of potency of competitive inhibitors of serine proteases was previously reported by Stroud and co-workers [Katz, B. A., Clark, J. M., Finer-Moore, J. S., Jenkins, T. E., Johnson, C. R., Ross, M. J., Luong, C., Moore, W. R., and Stroud, R. M. (1998) Nature 391, 608-612].
-===BETA-TRYPSIN COMPLEXED WITH APPU===
+Oxyanion-mediated inhibition of serine proteases.,Presnell SR, Patil GS, Mura C, Jude KM, Conley JM, Bertrand JA, Kam CM, Powers JC, Williams LD Biochemistry. 1998 Dec 1;37(48):17068-81. PMID:9836602<ref>PMID:9836602</ref>
-{{ABSTRACT_PUBMED_9836602}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1bjv" style="background-color:#fffaf0;"></div>
-[[1bjv]] is a 1 chain structure of [[Trypsin]] with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BJV OCA].
 ==See Also==
-*[[Trypsin|Trypsin]]
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:009836602</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Trypsin]]
+[[Category: Large Structures]]
-[[Category: Bertrand, J.]]
+[[Category: Bertrand J]]
-[[Category: Conley, J.]]
+[[Category: Conley J]]
-[[Category: Jude, K.]]
+[[Category: Jude K]]
-[[Category: Kam, C.]]
+[[Category: Kam C]]
-[[Category: Mura, C.]]
+[[Category: Mura C]]
-[[Category: Patil, G.]]
+[[Category: Patil G]]
-[[Category: Powers, J.]]
+[[Category: Powers J]]
-[[Category: Presnell, S.]]
+[[Category: Presnell S]]
-[[Category: Williams, L.]]
+[[Category: Williams L]]
-[[Category: Digestion]]
-[[Category: Hydrolase]]
-[[Category: Pancrea]]
-[[Category: Serine protease]]
-[[Category: Zymogen]]