1y3g

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[[Image:1y3g.gif|left|200px]]
 
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==Crystal Structure of a Silanediol Protease Inhibitor Bound to Thermolysin==
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The line below this paragraph, containing "STRUCTURE_1y3g", creates the "Structure Box" on the page.
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<StructureSection load='1y3g' size='340' side='right'caption='[[1y3g]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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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'>[[1y3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3G FirstGlance]. <br>
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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]] 2.1&#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=3PL:3-PHENYLPROPANAL'>3PL</scene>, <scene name='pdbligand=AMM:(2S)-2-{[(AMINOMETHYL)(DIHYDROXY)SILYL]METHYL}-4-METHYLPENTANAL'>AMM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1y3g| PDB=1y3g | 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=1y3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3g OCA], [https://pdbe.org/1y3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3g RCSB], [https://www.ebi.ac.uk/pdbsum/1y3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3g ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
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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/y3/1y3g_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=1y3g ConSurf].
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<div style="clear:both"></div>
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'''Crystal Structure of a Silanediol Protease Inhibitor Bound to Thermolysin'''
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==See Also==
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*[[Thermolysin 3D structures|Thermolysin 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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Dialkylsilanediols have been found to be an effective functional group for the design of active-site-directed protease inhibitors, including aspartic (HIV protease) and metallo (ACE and thermolysin) proteases. The use of silanediols is predicated on its resemblance to the hydrated carbonyl transition-state structure of amide hydrolysis. This concept has been tested by replacing the presumed tetrahedral carbon of a thermolysin substrate with a silanediol group, resulting in an inhibitor with an inhibition constant K(i) = 40 nM. The structure of the silanediol bound to the active site of thermolysin was found to have a conformation very similar to that of a corresponding phosphonamidate inhibitor (K(i) = 10 nM). In both cases, a single oxygen is within bonding distance to the active-site zinc ion, mimicking the presumed tetrahedral transition state. There are binding differences that appear to be related to the presence or absence of protons on the oxygens attached to the silicon or phosphorus. This is the first crystal structure of an organosilane bound to the active site of a protease.
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==About this Structure==
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1Y3G is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3G OCA].
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==Reference==
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Structural analysis of silanediols as transition-state-analogue inhibitors of the benchmark metalloprotease thermolysin., Juers DH, Kim J, Matthews BW, Sieburth SM, Biochemistry. 2005 Dec 20;44(50):16524-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16342943 16342943]
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[[Category: Bacillus thermoproteolyticus]]
[[Category: Bacillus thermoproteolyticus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Thermolysin]]
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[[Category: Juers DH]]
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[[Category: Juers, D H.]]
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[[Category: Kim J]]
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[[Category: Kim, J.]]
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[[Category: Matthews BW]]
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[[Category: Matthews, B W.]]
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[[Category: Sieburth SM]]
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[[Category: Sieburth, S M.]]
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[[Category: Silanediol protease inhibitor]]
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[[Category: Thermolysin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:50:20 2008''
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Current revision

Crystal Structure of a Silanediol Protease Inhibitor Bound to Thermolysin

PDB ID 1y3g

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