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1ppp

From Proteopedia

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[[Image:1ppp.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES==
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|PDB= 1ppp |SIZE=350|CAPTION= <scene name='initialview01'>1ppp</scene>, resolution 1.9&Aring;
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<StructureSection load='1ppp' size='340' side='right'caption='[[1ppp]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>
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<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPP FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.22.2 4.3.22.2] </span>
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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]] 1.9&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene></td></tr>
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|DOMAIN=
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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=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [https://pdbe.org/1ppp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [https://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppp ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PAPA1_CARPA PAPA1_CARPA]
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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/pp/1ppp_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=1ppp ConSurf].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES'''
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==See Also==
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*[[Papain|Papain]]
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__TOC__
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==Overview==
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</StructureSection>
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In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo &gt; 3 sigma(Fo)] were used for the structure solution and refinement. The papain structure was determined by means of the molecular replacement method, and then the inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference Fourier map. The complex structure was finally refined to R = 19.4% including 207 solvent molecules. Although this complex crystal (Form II) was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were significantly different from each other. By the calculation of accessible surface area for each complex atom, these two different binding modes were both shown to be tight enough to prevent the access of solvent molecules to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states which were derived from the crystal structures of Forms I and II. One of these, which corresponds to the binding mode simulated from Form I, was essentially the same as that observed in the crystal structure, and the other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the papain S subsites. The substrate specificity for the papain active site is discussed on the basis of the present results.
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[[Category: Carica papaya]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Ishida T]]
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1PPP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA].
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==Reference==
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Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites., Kim MJ, Yamamoto D, Matsumoto K, Inoue M, Ishida T, Mizuno H, Sumiya S, Kitamura K, Biochem J. 1992 Nov 1;287 ( Pt 3):797-803. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1445241 1445241]
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[[Category: Lyase]]
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[[Category: Single protein]]
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[[Category: Ishida, T.]]
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[[Category: hydrolase(sulfhydryl proteinase)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:02:52 2008''
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Current revision

CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES

PDB ID 1ppp

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