1y5b

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[[Image:1y5b.png|left|200px]]
 
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{{STRUCTURE_1y5b| PDB=1y5b | SCENE= }}
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==Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant==
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<StructureSection load='1y5b' size='340' side='right'caption='[[1y5b]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1y5b]] 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=1Y5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y5B FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
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<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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TL3:2,5-BIS-O-{4-[AMINO(IMINO)METHYL]PHENYL}-1,4 3,6-DIANHYDRO-D-GLUCITOL'>TL3</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5b OCA], [https://pdbe.org/1y5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y5b RCSB], [https://www.ebi.ac.uk/pdbsum/1y5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5b ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y5b_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1y5b ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases. To study the selectivity-determining features in detail, we used trypsin mutants in which the original binding site is gradually substituted to finally resemble the factor Xa binding pocket. The influence of these mutations has been analyzed on the binding of the closely related inhibitors. We present the crystal structures of the inhibitor complexes obtained by co-crystallizing an "intermediate" trypsin mutant. They could be determined to a resolution of up to 1.2 A, and we measured the inhibitory activity (K(i)) of each ligand against factor Xa, trypsin, and the various mutants. From these data we were able to derive a detailed structure-activity relationship which demonstrates the importance of aromatic interactions in protein-ligand recognition and their role in modulating enzyme selectivity. Pronounced preference is experienced to accommodate the benzamidine anchor with meta topology in the S(1) specificity pocket. One ligand possessing only para topology deviates strongly from the other members of the series and adopts a distinct binding mode addressing the S(1)' site instead of the distal S(3)/S(4) binding pocket.
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===Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant===
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Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions.,Di Fenza A, Heine A, Koert U, Klebe G ChemMedChem. 2007 Mar;2(3):297-308. PMID:17191291<ref>PMID:17191291</ref>
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{{ABSTRACT_PUBMED_17191291}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 1y5b" style="background-color:#fffaf0;"></div>
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[[1y5b]] 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=1Y5B OCA].
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==See Also==
==See Also==
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*[[Trypsin|Trypsin]]
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*[[Trypsin 3D structures|Trypsin 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:017191291</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Trypsin]]
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[[Category: Large Structures]]
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[[Category: Fenza, A Di.]]
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[[Category: Di Fenza A]]
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[[Category: Heine, A.]]
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[[Category: Heine A]]
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[[Category: Klebe, G.]]
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[[Category: Klebe G]]
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[[Category: Hydrolase]]
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[[Category: Serine protease]]
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[[Category: Serine proteinase]]
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Current revision

Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant

PDB ID 1y5b

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