1qrp

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[[Image:1qrp.gif|left|200px]]
 
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{{Structure
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==Human pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME==
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|PDB= 1qrp |SIZE=350|CAPTION= <scene name='initialview01'>1qrp</scene>, resolution 1.96&Aring;
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<StructureSection load='1qrp' size='340' side='right'caption='[[1qrp]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CH3:METHYL+GROUP'>CH3</scene>, <scene name='pdbligand=HFA:ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC+ACID'>HFA</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=PLE:LEUCINE+PHOSPHINIC+ACID'>PLE</scene>
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<table><tr><td colspan='2'>[[1qrp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRP FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.96&#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=HH0:METHYL+N-[(2S)-2-({(S)-HYDROXY[(1R)-3-METHYL-1-{[N-(3-METHYLBUTANOYL)-L-VALYL-L-VALYL]AMINO}BUTYL]PHOSPHORYL}OXY)-3-PHENYLPROPANOYL]-L-ALANYL-L-ALANINATE'>HH0</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=1qrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qrp OCA], [https://pdbe.org/1qrp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qrp RCSB], [https://www.ebi.ac.uk/pdbsum/1qrp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qrp 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=1qrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qrp OCA], [http://www.ebi.ac.uk/pdbsum/1qrp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qrp RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PEPA4_HUMAN PEPA4_HUMAN] Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent.
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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/qr/1qrp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1qrp 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 refined crystal structure of the complex between human pepsin and a synthetic phosphonate inhibitor, Iva-Val-Val-Leu(P)-(O)Phe-Ala-Ala-OMe [Iva = isovaleryl, Leu(P) = the phosphinic acid analog of L-leucine, (O)Phe = L-3-phenyllactic acid, OMe = methyl ester], is presented. The structure was refined using diffraction data between 30 and 1.96 A resolution to a final R factor ( summation operator| |F(o)| - |F(c)| | / summation operator|F(o)|, where |F(o)| and |F(c)| are the observed and calculated structure-factor amplitudes, respectively) of 20.0%. The interactions of the inhibitor with the enzyme show the locations of the binding sites on the enzyme from S4 to S3'. Modeling of the inhibitor binding to porcine pepsin shows very similar binding sites, except at S4. Comparison of the complex structure with the structures of related inhibitors bound to penicillopepsin helps to rationalize the observed differences in the binding constants. The convergence of reaction mechanisms and geometries in different families of proteinases is also discussed.
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'''HUMAN PEPSIN 3A IN COMPLEX WITH A PHOSPHONATE INHIBITOR IVA-VAL-VAL-LEU(P)-(O) PHE-ALA-ALA-OME'''
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Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.,Fujinaga M, Cherney MM, Tarasova NI, Bartlett PA, Hanson JE, James MN Acta Crystallogr D Biol Crystallogr. 2000 Mar;56(Pt 3):272-9. PMID:10713513<ref>PMID:10713513</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1qrp" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The refined crystal structure of the complex between human pepsin and a synthetic phosphonate inhibitor, Iva-Val-Val-Leu(P)-(O)Phe-Ala-Ala-OMe [Iva = isovaleryl, Leu(P) = the phosphinic acid analog of L-leucine, (O)Phe = L-3-phenyllactic acid, OMe = methyl ester], is presented. The structure was refined using diffraction data between 30 and 1.96 A resolution to a final R factor ( summation operator| |F(o)| - |F(c)| | / summation operator|F(o)|, where |F(o)| and |F(c)| are the observed and calculated structure-factor amplitudes, respectively) of 20.0%. The interactions of the inhibitor with the enzyme show the locations of the binding sites on the enzyme from S4 to S3'. Modeling of the inhibitor binding to porcine pepsin shows very similar binding sites, except at S4. Comparison of the complex structure with the structures of related inhibitors bound to penicillopepsin helps to rationalize the observed differences in the binding constants. The convergence of reaction mechanisms and geometries in different families of proteinases is also discussed.
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*[[Pepsin|Pepsin]]
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== References ==
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==About this Structure==
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<references/>
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1QRP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRP OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog., Fujinaga M, Cherney MM, Tarasova NI, Bartlett PA, Hanson JE, James MN, Acta Crystallogr D Biol Crystallogr. 2000 Mar;56(Pt 3):272-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10713513 10713513]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bartlett, P A.]]
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[[Category: Bartlett PA]]
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[[Category: Cherney, M M.]]
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[[Category: Cherney MM]]
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[[Category: Fujinaga, M.]]
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[[Category: Fujinaga M]]
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[[Category: Hanson, J E.]]
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[[Category: Hanson JE]]
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[[Category: James, M N.G.]]
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[[Category: James MNG]]
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[[Category: Tarasova, N I.]]
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[[Category: Tarasova NI]]
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[[Category: aspartic proteinase]]
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[[Category: phosphonate inhibitor]]
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[[Category: transition state analogue]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:18:02 2008''
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Current revision

Human pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME

PDB ID 1qrp

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