1h8l

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[[Image:1h8l.gif|left|200px]]
 
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==Duck Carboxypeptidase D Domain II in complex with GEMSA==
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The line below this paragraph, containing "STRUCTURE_1h8l", creates the "Structure Box" on the page.
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<StructureSection load='1h8l' size='340' side='right'caption='[[1h8l]], [[Resolution|resolution]] 2.60&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'>[[1h8l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lophonetta_specularioides Lophonetta specularioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H8L 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]] 2.6&#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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GEM:(2-GUANIDINOETHYLMERCAPTO)SUCCINIC+ACID'>GEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1h8l| PDB=1h8l | 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=1h8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h8l OCA], [https://pdbe.org/1h8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h8l RCSB], [https://www.ebi.ac.uk/pdbsum/1h8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h8l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CBPD_LOPSP CBPD_LOPSP]
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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/h8/1h8l_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=1h8l 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 three-dimensional crystal structure of duck carboxypeptidase D domain II has been solved in a complex with the peptidomimetic inhibitor, guanidinoethylmercaptosuccinic acid, occupying the specificity pocket. This structure allows a clear definition of the substrate binding sites and the substrate funnel-like access. The structure of domain II is the only one available from the regulatory carboxypeptidase family and can be used as a general template for its members. Here, it has been used to model the structures of domains I and III from the former protein and of human carboxypeptidase E. The models obtained show that the overall topology is similar in all cases, the main differences being local and because of insertions in non-regular loops. In both carboxypeptidase D domain I and carboxypeptidase E slightly different shapes of the access to the active site are predicted, implying some kind of structural selection of protein or peptide substrates. Furthermore, emplacement of the inhibitor structure in the active site of the constructed models showed that the inhibitor fits very well in all of them and that the relevant interactions observed with domain II are conserved in domain I and carboxypeptidase E but not in the non-active domain III because of the absence of catalytically indispensable residues in the latter protein. However, in domain III some of the residues potentially involved in substrate binding are well preserved, together with others of unknown roles, which also are highly conserved among all carboxypeptidases. These observations, taken together with others, suggest that domain III might play a role in the binding and presentation of proteins or peptide substrates, such as the pre-S domain of the large envelope protein of duck hepatitis B virus.
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'''DUCK CARBOXYPEPTIDASE D DOMAIN II IN COMPLEX WITH GEMSA'''
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The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases.,Aloy P, Companys V, Vendrell J, Aviles FX, Fricker LD, Coll M, Gomis-Ruth FX J Biol Chem. 2001 May 11;276(19):16177-84. Epub 2001 Feb 14. PMID:11278909<ref>PMID:11278909</ref>
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==Overview==
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The three-dimensional crystal structure of duck carboxypeptidase D domain II has been solved in a complex with the peptidomimetic inhibitor, guanidinoethylmercaptosuccinic acid, occupying the specificity pocket. This structure allows a clear definition of the substrate binding sites and the substrate funnel-like access. The structure of domain II is the only one available from the regulatory carboxypeptidase family and can be used as a general template for its members. Here, it has been used to model the structures of domains I and III from the former protein and of human carboxypeptidase E. The models obtained show that the overall topology is similar in all cases, the main differences being local and because of insertions in non-regular loops. In both carboxypeptidase D domain I and carboxypeptidase E slightly different shapes of the access to the active site are predicted, implying some kind of structural selection of protein or peptide substrates. Furthermore, emplacement of the inhibitor structure in the active site of the constructed models showed that the inhibitor fits very well in all of them and that the relevant interactions observed with domain II are conserved in domain I and carboxypeptidase E but not in the non-active domain III because of the absence of catalytically indispensable residues in the latter protein. However, in domain III some of the residues potentially involved in substrate binding are well preserved, together with others of unknown roles, which also are highly conserved among all carboxypeptidases. These observations, taken together with others, suggest that domain III might play a role in the binding and presentation of proteins or peptide substrates, such as the pre-S domain of the large envelope protein of duck hepatitis B virus.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1H8L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Anas_specularioides Anas specularioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H8L OCA].
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</div>
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<div class="pdbe-citations 1h8l" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases., Aloy P, Companys V, Vendrell J, Aviles FX, Fricker LD, Coll M, Gomis-Ruth FX, J Biol Chem. 2001 May 11;276(19):16177-84. Epub 2001 Feb 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11278909 11278909]
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*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
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[[Category: Anas specularioides]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Aviles, F X.]]
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__TOC__
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[[Category: Coll, M.]]
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</StructureSection>
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[[Category: Fricker, L D.]]
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[[Category: Large Structures]]
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[[Category: Gomis-Rueth, F X.]]
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[[Category: Lophonetta specularioides]]
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[[Category: Vendrell, J.]]
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[[Category: Aviles FX]]
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[[Category: Carboxypeptidase]]
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[[Category: Coll M]]
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[[Category: Hydrolase]]
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[[Category: Fricker LD]]
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[[Category: Zinc-dependent protease]]
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[[Category: Gomis-Rueth FX]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 18:34:25 2008''
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[[Category: Vendrell J]]

Current revision

Duck Carboxypeptidase D Domain II in complex with GEMSA

PDB ID 1h8l

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