4ubp

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[[Image:4ubp.gif|left|200px]]
 
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==STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION==
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The line below this paragraph, containing "STRUCTURE_4ubp", creates the "Structure Box" on the page.
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<StructureSection load='4ubp' size='340' side='right'caption='[[4ubp]], [[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'>[[4ubp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UBP 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=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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{{STRUCTURE_4ubp| PDB=4ubp | 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=4ubp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubp OCA], [https://pdbe.org/4ubp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ubp RCSB], [https://www.ebi.ac.uk/pdbsum/4ubp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/URE3_SPOPA URE3_SPOPA]
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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/ub/4ubp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=4ubp 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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The structure of Bacillus pasteurii urease inhibited with acetohydroxamic acid was solved and refined anisotropically using synchrotron X-ray cryogenic diffraction data (1.55 A resolution, 99.5% completeness, data redundancy = 26, R-factor = 15.1%, PDB code 4UBP). The two Ni ions in the active site are separated by a distance of 3.53 A. The structure clearly shows the binding mode of the inhibitor anion, symmetrically bridging the two Ni ions in the active site through the hydroxamate oxygen and chelating one Ni ion through the carbonyl oxygen. The flexible flap flanking the active site cavity is in the open conformation. The possible implications of the results on structure-based molecular design of new urease inhibitors are discussed.
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'''STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION'''
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The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution.,Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S J Biol Inorg Chem. 2000 Feb;5(1):110-8. PMID:10766443<ref>PMID:10766443</ref>
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==Overview==
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The structure of Bacillus pasteurii urease inhibited with acetohydroxamic acid was solved and refined anisotropically using synchrotron X-ray cryogenic diffraction data (1.55 A resolution, 99.5% completeness, data redundancy = 26, R-factor = 15.1%, PDB code 4UBP). The two Ni ions in the active site are separated by a distance of 3.53 A. The structure clearly shows the binding mode of the inhibitor anion, symmetrically bridging the two Ni ions in the active site through the hydroxamate oxygen and chelating one Ni ion through the carbonyl oxygen. The flexible flap flanking the active site cavity is in the open conformation. The possible implications of the results on structure-based molecular design of new urease inhibitors are discussed.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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4UBP is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBP OCA].
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</div>
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<div class="pdbe-citations 4ubp" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution., Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S, J Biol Inorg Chem. 2000 Feb;5(1):110-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10766443 10766443]
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*[[Urease 3D structures|Urease 3D structures]]
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[[Category: Protein complex]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Sporosarcina pasteurii]]
[[Category: Sporosarcina pasteurii]]
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[[Category: Urease]]
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[[Category: Benini S]]
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[[Category: Benini, S.]]
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[[Category: Ciurli S]]
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[[Category: Ciurli, S.]]
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[[Category: Mangani S]]
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[[Category: Mangani, S.]]
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[[Category: Rypniewski WR]]
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[[Category: Rypniewski, W R.]]
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[[Category: Wilson KS]]
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[[Category: Wilson, K S.]]
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[[Category: Acetohydroxamic acid]]
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[[Category: Bacillus pasteurii]]
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[[Category: Metalloenzyme]]
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[[Category: Nickel]]
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[[Category: Urease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:30:50 2008''
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Current revision

STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION

PDB ID 4ubp

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