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3q00

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Current revision (13:36, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3q00' size='340' side='right'caption='[[3q00]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='3q00' size='340' side='right'caption='[[3q00]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q00]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q00 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q00]] 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=3Q00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q00 FirstGlance]. <br>
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</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=PEU:2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL'>PEU</scene>, <scene name='pdbligand=PMJ:N~2~-(BENZYLSULFONYL)-D-ARGINYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE'>PMJ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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]] 1.7&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1v2k|1v2k]], [[3plk|3plk]], [[3plp|3plp]], [[3pm3|3pm3]], [[3pwb|3pwb]], [[3pwc|3pwc]], [[3pyh|3pyh]]</div></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=PEU:2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL'>PEU</scene>, <scene name='pdbligand=PMJ:N~2~-(BENZYLSULFONYL)-D-ARGINYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE'>PMJ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></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=3q00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q00 OCA], [https://pdbe.org/3q00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q00 RCSB], [https://www.ebi.ac.uk/pdbsum/3q00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q00 ProSAT]</span></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=3q00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q00 OCA], [https://pdbe.org/3q00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q00 RCSB], [https://www.ebi.ac.uk/pdbsum/3q00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q00 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
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Abstract A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.
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Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.,Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Brauer U, Ursel C, Steinmetzer P, Sturzebecher J, Schweinitz A, Steinmetzer T, Stubbs MT Biol Chem. 2014 Jul 1;395(7-8):891-903. doi: 10.1515/hsz-2014-0158. PMID:25003390<ref>PMID:25003390</ref>
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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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<div class="pdbe-citations 3q00" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Trypsin 3D structures|Trypsin 3D structures]]
*[[Trypsin 3D structures|Trypsin 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bovin]]
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[[Category: Bos taurus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Trypsin]]
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[[Category: Kolenko P]]
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[[Category: Kolenko, P]]
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[[Category: Neumann P]]
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[[Category: Neumann, P]]
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[[Category: Stubbs MT]]
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[[Category: Stubbs, M T]]
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[[Category: Tziridis A]]
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[[Category: Tziridis, A]]
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[[Category: Duodenum]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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[[Category: Protein binding]]
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[[Category: Trypsin-like serine protease]]
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Current revision

Bovine trypsin variant X(tripleGlu217Ile227) in complex with small molecule inhibitor

PDB ID 3q00

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