2ayw: Difference between revisions
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==Crystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution== | ==Crystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution== | ||
<StructureSection load='2ayw' size='340' side='right' caption='[[2ayw]], [[Resolution|resolution]] 0.97Å' scene=''> | <StructureSection load='2ayw' size='340' side='right'caption='[[2ayw]], [[Resolution|resolution]] 0.97Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2ayw]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2ayw]] 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=2AYW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AYW FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ONO:2-[2-({[4-(DIAMINOMETHYL)PHENYL]AMINO}CARBONYL)-6-METHOXYPYRIDIN-3-YL]-5-{[(1-FORMYL-2,2-DIMETHYLPROPYL)AMINO]CARBONYL}BENZOIC+ACID'>ONO</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.97Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ONO:2-[2-({[4-(DIAMINOMETHYL)PHENYL]AMINO}CARBONYL)-6-METHOXYPYRIDIN-3-YL]-5-{[(1-FORMYL-2,2-DIMETHYLPROPYL)AMINO]CARBONYL}BENZOIC+ACID'>ONO</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ayw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ayw OCA], [https://pdbe.org/2ayw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ayw RCSB], [https://www.ebi.ac.uk/pdbsum/2ayw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ayw ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ay/2ayw_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ay/2ayw_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2ayw" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2ayw" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Trypsin 3D structures|Trypsin 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Bos taurus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Betzel | [[Category: Betzel C]] | ||
[[Category: Bisacchi | [[Category: Bisacchi GS]] | ||
[[Category: Chang | [[Category: Chang C]] | ||
[[Category: Einspahr | [[Category: Einspahr HM]] | ||
[[Category: Jacobson | [[Category: Jacobson BL]] | ||
[[Category: Kaur | [[Category: Kaur P]] | ||
[[Category: Perbandt | [[Category: Perbandt M]] | ||
[[Category: Sherawat | [[Category: Sherawat M]] | ||
[[Category: Singh | [[Category: Singh TP]] | ||
[[Category: Slusarchyk | [[Category: Slusarchyk WA]] | ||
Latest revision as of 11:18, 25 October 2023
Crystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolutionCrystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structure of the complex formed between bovine beta-trypsin and the highly potent synthetic inhibitor 2-{3'-[5'-methoxy-2'-(N-p-diaminomethylphenyl)amido]-1'-pyrido}-5-(N-2-t -butylethanol)amidobenzoic acid (C(28)H(32)N(5)O(6)) has been determined at 0.97 A resolution. X-ray intensity data were collected to 0.97 A under cryocooled conditions. The structure was refined anisotropically using REFMAC5 and SHELX-97 to R(cryst) factors of 13.4 and 12.6% and R(free) factors of 15.7 and 16.3%, respectively. Several regions of the main chain and side chains that have not been previously observed were clearly defined in the present structure. H atoms are indicated as significant peaks in an |F(o) - F(c)| difference map, which accounts for an estimated 35% of all H atoms at the 2.5sigma level. The C, N and O atoms are definitively differentiated in the electron-density maps. The amido part of the inhibitor occupies the specificity pocket and the remainder fills the remaining part of the ligand-binding cleft and interacts with the enzyme through an extensive network of hydrogen bonds. The inhibitor distorts the stereochemistry of the catalytic triad, Ser195-His57-Asp102, thereby blocking the proton-relay process of the active site by preventing the formation of the crucial hydrogen bond between His57 N(delta1) and Asp102 O(delta1). Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.,Sherawat M, Kaur P, Perbandt M, Betzel C, Slusarchyk WA, Bisacchi GS, Chang C, Jacobson BL, Einspahr HM, Singh TP Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):500-7. Epub 2007, Mar 16. PMID:17372355[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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