3l6n: Difference between revisions

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-{{Seed}}
-[[Image:3l6n.jpg|left|200px]]
-<!--
+==Crystal structure of metallo-beta-lactamase IND-7==
-The line below this paragraph, containing "STRUCTURE_3l6n", creates the "Structure Box" on the page.
+<StructureSection load='3l6n' size='340' side='right'caption='[[3l6n]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3l6n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chryseobacterium_indologenes Chryseobacterium indologenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L6N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L6N FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3l6n|  PDB=3l6n  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3l6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6n OCA], [https://pdbe.org/3l6n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l6n RCSB], [https://www.ebi.ac.uk/pdbsum/3l6n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6n ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A4GRB2_9FLAO A4GRB2_9FLAO]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/3l6n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3l6n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray crystal structure of metallo-beta-lactamase from Chryseobacterium indologenes IND-7 was determined at a resolution of 1.65 A. The overall structure adopted a four-layered alphabeta/betaalpha sandwich structure with a dinuclear zinc(II) active site, in which the zinc(II) ions were denoted as Zn1 and Zn2. The overall structure of IND-7 is analogous to those of subclass B1 metallo-beta-lactamases, as determined by X-ray crystallography. A significant structural difference, however, was observed in the dinuclear zinc(II) active site: the coordination geometry around Zn1 changed from tetrahedral, found in other subclass B1 metallo-beta-lactamases, to distorted trigonal bipyramidal, whereas that of Zn2 changed from trigonal bipyramidal to tetrahedral. Arg121(101), which is located in the vicinity of the dinuclear zinc(II) active site, may affect the binding affinity of Zn2 due to an electronic repulsion between the zinc(II) ion(s) and a positively charged guanidyl group of Arg121(101). Moreover, the hydrogen-bonding interaction of Arg121 with Ser71(53), which is conserved in IND-1, IND-3 and IND-5-IND-7, appeared to have important consequences for the binding affinity of Zn2 in conjunction with the above electrostatic effect.
-===Crystal structure of metallo-beta-lactamase IND-7===
+Structure of metallo-beta-lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution.,Yamaguchi Y, Takashio N, Wachino J, Yamagata Y, Arakawa Y, Matsuda K, Kurosaki H J Biochem. 2010 Jun;147(6):905-15. Epub 2010 Mar 19. PMID:20305272<ref>PMID:20305272</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3l6n" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20305272}}, adds the Publication Abstract to the page
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20305272 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20305272}}
+__TOC__
+</StructureSection>
-==About this Structure==
-L6N is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chryseobacterium_indologenes Chryseobacterium indologenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L6N OCA].
-==Reference==
-<ref group="xtra">PMID:20305272</ref><references group="xtra"/>
-[[Category: Beta-lactamase]]
 [[Category: Chryseobacterium indologenes]]
-[[Category: Kurosaki, H.]]
+[[Category: Large Structures]]
-[[Category: Yamagata, Y.]]
+[[Category: Kurosaki H]]
-[[Category: Yamaguchi, Y.]]
+[[Category: Yamagata Y]]
-[[Category: Antibiotics resistance]]
+[[Category: Yamaguchi Y]]
-[[Category: Hydolase]]
-[[Category: Hydrolase]]
-[[Category: Metallo-beta-lactamase]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 14 09:38:09 2010''