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3nk8

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Current revision (10:00, 14 February 2024) (edit) (undo)
 
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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3nk8]] 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=3NK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NK8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3nk8]] 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=3NK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NK8 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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=JKZ:4-(TRIFLUOROMETHYL)-1,5,6,7-TETRAHYDRO-2H-CYCLOPENTA[B]PYRIDIN-2-ONE'>JKZ</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]] 1.15&#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;'>[[3nkk|3nkk]]</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=JKZ:4-(TRIFLUOROMETHYL)-1,5,6,7-TETRAHYDRO-2H-CYCLOPENTA[B]PYRIDIN-2-ONE'>JKZ</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=3nk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nk8 OCA], [https://pdbe.org/3nk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nk8 RCSB], [https://www.ebi.ac.uk/pdbsum/3nk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nk8 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=3nk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nk8 OCA], [https://pdbe.org/3nk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nk8 RCSB], [https://www.ebi.ac.uk/pdbsum/3nk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nk8 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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(19) F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description. Proteins 2010. (c) 2010 Wiley-Liss, Inc.
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Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments.,Vulpetti A, Schiering N, Dalvit C Proteins. 2010 Dec;78(16):3281-91. doi: 10.1002/prot.22836. PMID:20886466<ref>PMID:20886466</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 3nk8" 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>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Trypsin]]
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[[Category: Dalvit C]]
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[[Category: Dalvit, C]]
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[[Category: Schiering N]]
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[[Category: Schiering, N]]
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[[Category: Vulpetti A]]
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[[Category: Vulpetti, A]]
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[[Category: Beta barrel]]
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[[Category: Calcium binding]]
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[[Category: Chymotrypsin double beta barrel]]
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[[Category: Hydrolase]]
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[[Category: Pancreas-duodenum]]
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[[Category: Peptide hydrolase]]
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Current revision

Trypsin in complex with fluorine-containing fragment

PDB ID 3nk8

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