3wd3: Difference between revisions

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-{{STRUCTURE_3wd3|  PDB=3wd3  |  SCENE=  }}
-===Serratia marcescens Chitinase B complexed with azide inhibitor===
-{{ABSTRACT_PUBMED_24043811}}
-==About this Structure==
+==Serratia marcescens Chitinase B complexed with azide inhibitor==
-[[3wd3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WD3 OCA].
+<StructureSection load='3wd3' size='340' side='right'caption='[[3wd3]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3wd3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WD3 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1L:[2-[[(2S)-1-[BIS(PHENYLMETHYL)AMINO]-5-[[N-(METHYLCARBAMOYL)CARBAMIMIDOYL]AMINO]-1-OXIDANYLIDENE-PENTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-DIAZONIO-AZANIDE'>A1L</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3wd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wd3 OCA], [https://pdbe.org/3wd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wd3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wd3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CHIB_SERMA CHIB_SERMA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marcescens chitinase B (SmChiB)-templated syn-triazole inhibitor generated in situ from an azide-bearing inhibitor and an alkyne fragment. Several in situ click chemistry studies have been reported. Although some mechanistic evidence has been obtained, such as X-ray analysis of [protein]-["click ligand"] complexes, indicating that proteins act as both mold and template between unique pairs of azide and alkyne fragments, to date, observations have been based solely on "postclick" structural information. Here, we describe crystal structures of SmChiB complexed with an azide ligand and an O-allyl oxime fragment as a mimic of a click partner, revealing a mechanism for accelerating syn-triazole formation, which allows generation of its own distinct inhibitor. We have also performed density functional theory calculations based on the X-ray structure to explore the acceleration of the Huisgen cycloaddition by SmChiB. The density functional theory calculations reasonably support that SmChiB plays a role by the cage effect during the pretranslation and posttranslation states of selective syn-triazole click formation.
-==Reference==
+Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor.,Hirose T, Maita N, Gouda H, Koseki J, Yamamoto T, Sugawara A, Nakano H, Hirono S, Shiomi K, Watanabe T, Taniguchi H, Sharpless KB, Omura S, Sunazuka T Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):15892-7. doi:, 10.1073/pnas.1315049110. Epub 2013 Sep 16. PMID:24043811<ref>PMID:24043811</ref>
-<ref group="xtra">PMID:024043811</ref><references group="xtra"/><references/>
-[[Category: Chitinase]]
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3wd3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Chitinase 3D structures|Chitinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Serratia marcescens]]
-[[Category: Gouda, H.]]
+[[Category: Gouda H]]
-[[Category: Hirono, S.]]
+[[Category: Hirono S]]
-[[Category: Hirose, T.]]
+[[Category: Hirose T]]
-[[Category: Koseki, J.]]
+[[Category: Koseki J]]
-[[Category: Maita, N.]]
+[[Category: Maita N]]
-[[Category: Nakano, H.]]
+[[Category: Nakano H]]
-[[Category: Omura, S.]]
+[[Category: Omura S]]
-[[Category: Sharpless, K B.]]
+[[Category: Sharpless KB]]
-[[Category: Shiomi, K.]]
+[[Category: Shiomi K]]
-[[Category: Sugawara, A.]]
+[[Category: Sugawara A]]
-[[Category: Sunazuka, T.]]
+[[Category: Sunazuka T]]
-[[Category: Taniguchi, H.]]
+[[Category: Taniguchi H]]
-[[Category: Watanabe, T.]]
+[[Category: Watanabe T]]
-[[Category: Yamamoto, T.]]
+[[Category: Yamamoto T]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Tim barrel]]