1may: Difference between revisions

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-[[Image:1may.gif|left|200px]]<br /><applet load="1may" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1may, resolution 1.8&Aring;" />
-'''BETA-TRYPSIN PHOSPHONATE INHIBITED'''<br />
-==Overview==
+==BETA-TRYPSIN PHOSPHONATE INHIBITED==
-X-ray structures of trypsin from bovine pancreas inactivated by diphenyl, [N-(benzyloxycarbonyl)amino](4-amidinophenyl)methanephosphonate, [Z-(4-AmPhGly)P(OPh)2] were determined at 113 and 293 K to 1.8 angstrom, resolution and refined to R factors of 0.211 (113 K) and 0. 178 (293 K)., The structures reveal a tetrahedral phosphorus covalently bonded to the O, gamma of the active site serine. Covalent bond formation is accompanied by, the loss of both phenoxy groups. The D-stereoisomer of, Z-(4-AmPhGly)P-(OPh)2 is not observed in the complex. The L-stereoisomer, of the inhibitor forms contacts with several residues in the trypsin, active site. One of the phosphonate oxygens is inserted into the oxyanion, hole and forms hydrogen bonds to the amides of Gly193, Asp194, and Ser195., The second phosphonate oxygen forms hydrogen bonds to N epsilon 2 of His, 57. The p-amidinophenylglycine moiety binds into the trypsin primary, specificity pocket, interacting with Asp189. The amide forms a hydrogen, bond to the carbonyl oxygen atom of Ser214. The inhibitor moiety, from the, 113 K structure of trypsin inactivated by the reaction product of, Z-(4-AmPhGly)P(OPh)2, was docked into human thrombin [Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., &amp; Hofsteenge, J. (1989) EMBO J. 8, 3467-3475] and energy minimized. The inhibitor fits well into the thrombin, active site, forming favorable contacts similar to those in the trypsin, complex with no bad contacts.
+<StructureSection load='1may' size='340' side='right'caption='[[1may]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1may]] 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=1MAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MAY 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=ZAP:[N-(BENZYLOXYCARBONYL)AMINO](4-AMIDINOPHENYL)METHANE-PHOSPHONATE'>ZAP</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=1may FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1may OCA], [https://pdbe.org/1may PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1may RCSB], [https://www.ebi.ac.uk/pdbsum/1may PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1may 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/ma/1may_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=1may ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+X-ray structures of trypsin from bovine pancreas inactivated by diphenyl [N-(benzyloxycarbonyl)amino](4-amidinophenyl)methanephosphonate [Z-(4-AmPhGly)P(OPh)2] were determined at 113 and 293 K to 1.8 angstrom resolution and refined to R factors of 0.211 (113 K) and 0. 178 (293 K). The structures reveal a tetrahedral phosphorus covalently bonded to the O gamma of the active site serine. Covalent bond formation is accompanied by the loss of both phenoxy groups. The D-stereoisomer of Z-(4-AmPhGly)P-(OPh)2 is not observed in the complex. The L-stereoisomer of the inhibitor forms contacts with several residues in the trypsin active site. One of the phosphonate oxygens is inserted into the oxyanion hole and forms hydrogen bonds to the amides of Gly193, Asp194, and Ser195. The second phosphonate oxygen forms hydrogen bonds to N epsilon 2 of His 57. The p-amidinophenylglycine moiety binds into the trypsin primary specificity pocket, interacting with Asp189. The amide forms a hydrogen bond to the carbonyl oxygen atom of Ser214. The inhibitor moiety, from the 113 K structure of trypsin inactivated by the reaction product of Z-(4-AmPhGly)P(OPh)2, was docked into human thrombin [Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., &amp; Hofsteenge, J. (1989) EMBO J. 8, 3467-3475] and energy minimized. The inhibitor fits well into the thrombin active site, forming favorable contacts similar to those in the trypsin complex with no bad contacts.
-==About this Structure==
+Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models.,Bertrand JA, Oleksyszyn J, Kam CM, Boduszek B, Presnell S, Plaskon RR, Suddath FL, Powers JC, Williams LD Biochemistry. 1996 Mar 12;35(10):3147-55. PMID:8605148<ref>PMID:8605148</ref>
-MAY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with CA and ZAP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MAY OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models., Bertrand JA, Oleksyszyn J, Kam CM, Boduszek B, Presnell S, Plaskon RR, Suddath FL, Powers JC, Williams LD, Biochemistry. 1996 Mar 12;35(10):3147-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8605148 8605148]
+</div>
+<div class="pdbe-citations 1may" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Trypsin]]
+[[Category: Bertrand J]]
-[[Category: Bertrand, J.]]
+[[Category: Boduszek B]]
-[[Category: Boduszek, B.]]
+[[Category: Kam C]]
-[[Category: Kam, C.]]
+[[Category: Oleksyszyn J]]
-[[Category: Oleksyszyn, J.]]
+[[Category: Plaskon R]]
-[[Category: Plaskon, R.]]
+[[Category: Powers J]]
-[[Category: Powers, J.]]
+[[Category: Presnell S]]
-[[Category: Presnell, S.]]
+[[Category: Suddath F]]
-[[Category: Suddath, F.]]
+[[Category: Williams L]]
-[[Category: Williams, L.]]
-[[Category: CA]]
-[[Category: ZAP]]
-[[Category: digestion]]
-[[Category: hydrolase]]
-[[Category: pancreas]]
-[[Category: serine protease]]
-[[Category: zymogen]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:17:19 2007''