1xep

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[[Image:1xep.gif|left|200px]]
 
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==Catechol in complex with T4 lysozyme L99A/M102Q==
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The line below this paragraph, containing "STRUCTURE_1xep", creates the "Structure Box" on the page.
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<StructureSection load='1xep' size='340' side='right'caption='[[1xep]], [[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'>[[1xep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XEP 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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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{{STRUCTURE_1xep| PDB=1xep | 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=1xep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xep OCA], [https://pdbe.org/1xep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xep RCSB], [https://www.ebi.ac.uk/pdbsum/1xep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xep ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
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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/xe/1xep_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=1xep ConSurf].
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<div style="clear:both"></div>
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'''Catechol in complex with T4 lysozyme L99A/M102Q'''
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==See Also==
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==Overview==
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<references/>
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Molecular docking is widely used to predict novel lead compounds for drug discovery. Success depends on the quality of the docking scoring function, among other factors. An imperfect scoring function can mislead by predicting incorrect ligand geometries or by selecting nonbinding molecules over true ligands. These false-positive hits may be considered "decoys". Although these decoys are frustrating, they potentially provide important tests for a docking algorithm; the more subtle the decoy, the more rigorous the test. Indeed, decoy databases have been used to improve protein structure prediction algorithms and protein-protein docking algorithms. Here, we describe 20 geometric decoys in five enzymes and 166 "hit list" decoys-i.e., molecules predicted to bind by our docking program that were tested and found not to do so-for beta-lactamase and two cavity sites in lysozyme. Especially in the cavity sites, which are very simple, these decoys highlight particular weaknesses in our scoring function. We also consider the performance of five other widely used docking scoring functions against our geometric and hit list decoys. Intriguingly, whereas many of these other scoring functions performed better on the geometric decoys, they typically performed worse on the hit list decoys, often highly ranking molecules that seemed to poorly complement the model sites. Several of these "hits"from the other scoring functions were tested experimentally and found, in fact, to be decoys. Collectively, these decoys provide a tool for the development and improvement of molecular docking scoring functions. Such improvements may, in turn, be rapidly tested experimentally against these and related experimental systems, which are well-behaved in assays and for structure determination.
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia virus T4]]
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1XEP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XEP OCA].
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[[Category: Large Structures]]
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[[Category: Brenk R]]
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==Reference==
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[[Category: Graves AP]]
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Decoys for docking., Graves AP, Brenk R, Shoichet BK, J Med Chem. 2005 Jun 2;48(11):3714-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15916423 15916423]
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[[Category: Shoichet BK]]
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[[Category: Enterobacteria phage t4]]
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[[Category: Lysozyme]]
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[[Category: Single protein]]
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[[Category: Brenk, R.]]
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[[Category: Graves, A P.]]
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[[Category: Shoichet, B K.]]
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[[Category: Bacteriolytic enzyme]]
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[[Category: Glycosidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:55:55 2008''
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Current revision

Catechol in complex with T4 lysozyme L99A/M102Q

PDB ID 1xep

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