1v6d

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(New page: 200px<br /><applet load="1v6d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v6d, resolution 1.90&Aring;" /> '''The crystal structur...)
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[[Image:1v6d.gif|left|200px]]<br /><applet load="1v6d" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1v6d, resolution 1.90&Aring;" />
 
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'''The crystal structure of the trypsin complex with synthetic heterochiral peptide'''<br />
 
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==Overview==
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==The crystal structure of the trypsin complex with synthetic heterochiral peptide==
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Designed synthetic heterochiral peptides, when added to porcine trypsin, resulted in reduction of enzyme activity. The crystal structure of a, complex formed between porcine trypsin and a heterochiral hepta peptide, Boc-Pro-DAsp-Aib-Leu-Aib-Leu-Ala-NHMe has been determined at 1.9 A, resolution. The hepta peptide does not bind at the active site, but is, located in the interstitial region, and interacts with the calcium-binding, loop (residues 60-80). The bound peptide interacts with the active site, residue Ser195 through an acetate ion, and with Lys 60 mediated by water, molecules. The structure, when compared with the other trypsin-peptide, complexes, suggests that the flexibility of surface loops, concerted, movement of the loops towards the active site, and the interaction of the, bound peptide with Lys 60, may be responsible for the reduction in enzyme, activity. This study provides a structural evidence for the earlier, biochemical observation regarding the role of surface loops in the, catalysis of the enzyme.
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<StructureSection load='1v6d' size='340' side='right'caption='[[1v6d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1v6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V6D FirstGlance]. <br>
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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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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AIB:ALPHA-AMINOISOBUTYRIC+ACID'>AIB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene>, <scene name='pdbligand=TBF:TERT-BUTYL+FORMATE'>TBF</scene></td></tr>
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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=1v6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v6d OCA], [https://pdbe.org/1v6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v6d RCSB], [https://www.ebi.ac.uk/pdbsum/1v6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v6d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRYP_PIG TRYP_PIG]
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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/v6/1v6d_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=1v6d 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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Designed synthetic heterochiral peptides, when added to porcine trypsin, resulted in reduction of enzyme activity. The crystal structure of a complex formed between porcine trypsin and a heterochiral hepta peptide Boc-Pro-DAsp-Aib-Leu-Aib-Leu-Ala-NHMe has been determined at 1.9 A resolution. The hepta peptide does not bind at the active site, but is located in the interstitial region, and interacts with the calcium-binding loop (residues 60-80). The bound peptide interacts with the active site residue Ser195 through an acetate ion, and with Lys 60 mediated by water molecules. The structure, when compared with the other trypsin-peptide complexes, suggests that the flexibility of surface loops, concerted movement of the loops towards the active site, and the interaction of the bound peptide with Lys 60, may be responsible for the reduction in enzyme activity. This study provides a structural evidence for the earlier biochemical observation regarding the role of surface loops in the catalysis of the enzyme.
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==About this Structure==
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Secondary binding site of trypsin: revealed by crystal structure of trypsin-peptide complex.,Shamaladevi N, Pattabhi V J Biomol Struct Dyn. 2005 Jun;22(6):635-42. PMID:15842169<ref>PMID:15842169</ref>
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1V6D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with CA and ACT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V6D OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Secondary binding site of trypsin: revealed by crystal structure of trypsin-peptide complex., Shamaladevi N, Pattabhi V, J Biomol Struct Dyn. 2005 Jun;22(6):635-42. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15842169 15842169]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1v6d" style="background-color:#fffaf0;"></div>
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[[Category: Sus scrofa]]
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[[Category: Trypsin]]
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[[Category: Pattabhi, V.]]
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[[Category: Shamaladevi, N.]]
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[[Category: ACT]]
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[[Category: CA]]
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[[Category: synthetic peptide]]
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[[Category: trypsin complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:28:11 2007''
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==See Also==
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*[[Trypsin 3D structures|Trypsin 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Sus scrofa]]
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[[Category: Pattabhi V]]
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[[Category: Shamaladevi N]]

Current revision

The crystal structure of the trypsin complex with synthetic heterochiral peptide

PDB ID 1v6d

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