3d4f

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{{Seed}}
 
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[[Image:3d4f.jpg|left|200px]]
 
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==SHV-1 beta-lactamase complex with LN1-255==
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The line below this paragraph, containing "STRUCTURE_3d4f", creates the "Structure Box" on the page.
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<StructureSection load='3d4f' size='340' side='right'caption='[[3d4f]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3d4f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D4F FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.55&#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=LN1:(3R)-4-{[(3,4-DIHYDROXYPHENYL)ACETYL]OXY}-N-(2-FORMYLINDOLIZIN-3-YL)-3-SULFINO-D-VALINE'>LN1</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene></td></tr>
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{{STRUCTURE_3d4f| PDB=3d4f | SCENE= }}
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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=3d4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d4f OCA], [https://pdbe.org/3d4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d4f RCSB], [https://www.ebi.ac.uk/pdbsum/3d4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d4f ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]
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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/d4/3d4f_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=3d4f 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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In an effort to devise strategies for overcoming bacterial beta-lactamases, we studied LN-1-255, a 6-alkylidene-2'-substituted penicillin sulfone inhibitor. By possessing a catecholic functionality that resembles a natural bacterial siderophore, LN-1-255 is unique among beta-lactamase inhibitors. LN-1-255 combined with piperacillin was more potent against Escherichia coli DH10B strains bearing bla(SHV) extended-spectrum and inhibitor-resistant beta-lactamases than an equivalent amount of tazobactam and piperacillin. In addition, LN-1-255 significantly enhanced the activity of ceftazidime and cefpirome against extended-spectrum cephalosporin and Sme-1 containing carbapenem-resistant clinical strains. LN-1-255 inhibited SHV-1 and SHV-2 beta-lactamases with nm affinity (K(I) = 110 +/- 10 and 100 +/- 10 nm, respectively). When LN-1-255 inactivated SHV beta-lactamases, a single intermediate was detected by mass spectrometry. The crystal structure of LN-1-255 in complex with SHV-1 was determined at 1.55A resolution. Interestingly, this novel inhibitor forms a bicyclic aromatic intermediate with its carbonyl oxygen pointing out of the oxyanion hole and forming hydrogen bonds with Lys-234 and Ser-130 in the active site. Electron density for the "tail" of LN-1-255 is less ordered and modeled in two conformations. Both conformations have the LN-1-255 carboxyl group interacting with Arg-244, yet the remaining tails of the two conformations diverge. The observed presence of the bicyclic aromatic intermediate with its carbonyl oxygen positioned outside of the oxyanion hole provides a rationale for the stability of this inhibitory intermediate. The 2'-substituted penicillin sulfone, LN-1-255, is proving to be an important lead compound for novel beta-lactamase inhibitor design.
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===SHV-1 beta-lactamase complex with LN1-255===
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Strategic design of an effective beta-lactamase inhibitor: LN-1-255, a 6-alkylidene-2'-substituted penicillin sulfone.,Pattanaik P, Bethel CR, Hujer AM, Hujer KM, Distler AM, Taracila M, Anderson VE, Fritsche TR, Jones RN, Pagadala SR, van den Akker F, Buynak JD, Bonomo RA J Biol Chem. 2009 Jan 9;284(2):945-53. Epub 2008 Oct 27. PMID:18955486<ref>PMID:18955486</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 3d4f" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18955486}}, adds the Publication Abstract to the page
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*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18955486 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18955486}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3D4F is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D4F OCA].
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==Reference==
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<ref group="xtra">PMID:18955486</ref><references group="xtra"/>
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[[Category: Beta-lactamase]]
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[[Category: Klebsiella pneumoniae]]
[[Category: Klebsiella pneumoniae]]
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[[Category: Akker, F van den.]]
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[[Category: Large Structures]]
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[[Category: Bethel, C R.]]
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[[Category: Bethel CR]]
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[[Category: Bonomo, R A.]]
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[[Category: Bonomo RA]]
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[[Category: Buynak, J D.]]
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[[Category: Buynak JD]]
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[[Category: Hujer, A M.]]
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[[Category: Hujer AM]]
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[[Category: Pattanaik, P.]]
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[[Category: Pattanaik P]]
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[[Category: Antibiotic resistance]]
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[[Category: Van den Akker F]]
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[[Category: Beta-lactamase inhibitor]]
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[[Category: Drug design]]
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[[Category: Hydrolase]]
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[[Category: Plasmid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 12:40:11 2009''
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Current revision

SHV-1 beta-lactamase complex with LN1-255

PDB ID 3d4f

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