1xep

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[[Image:1xep.gif|left|200px]]
 
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{{Structure
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==Catechol in complex with T4 lysozyme L99A/M102Q==
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|PDB= 1xep |SIZE=350|CAPTION= <scene name='initialview01'>1xep</scene>, resolution 1.55&Aring;
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<StructureSection load='1xep' size='340' side='right'caption='[[1xep]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene> and <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>
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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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|ACTIVITY= [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]
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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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|GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4])
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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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}}
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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/Bacteriophage_t4 Bacteriophage 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: Bacteriophage 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: BME]]
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[[Category: CAQ]]
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[[Category: PO4]]
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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 Thu Mar 20 15:08:48 2008''
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Current revision

Catechol in complex with T4 lysozyme L99A/M102Q

PDB ID 1xep

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