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1ivl

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[[Image:1ivl.gif|left|200px]]<br /><applet load="1ivl" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ivl, resolution 2.17&Aring;" />
 
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'''THE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHIC ANALYSIS OF THE VL DOMAIN CONFIRMS THE STRUCTURAL MODEL'''<br />
 
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==Overview==
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==THE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHIC ANALYSIS OF THE VL DOMAIN CONFIRMS THE STRUCTURAL MODEL==
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In a protein design approach the molecular model of an artificial antibody Fv fragment was generated with predicted complementarity to part of the known crystal structure of chicken egg-white cystatin. The model of the Fv fragment was based on the three-dimensional structure of the anti-lysozyme antibody HyHEL-10, which was modified by substituting amino acid side-chains in the complementarity-determining regions (CDRs) as well as the framework without altering the backbone. In the course of crystallization experiments with the bacterially produced Fv fragment crystals of the VL domain alone were obtained. These crystals diffracted X-rays to a resolution of 2.17 A and were shown to belong to the space group P2(1)2(1)2(1) with unit cell dimensions a = 46.89 A, b = 58.05 A, c = 83.22 A containing two VL monomers in the asymmetric unit. The crystal structure was solved by molecular replacement and refined to a crystallographic R-factor of 17.5%. The two VL monomers exhibit an asymmetric mode of association, which is different from other crystallized VL domains described before and shows the peculiar feature of an isopropanol precipitant molecule buried at the interface. Both VL structures reveal a high level of similarity to the predicted three-dimensional model. With the exception of two loop segments in the framework region that are involved in crystal packing contacts, the backbone structures of the two VL monomers in the crystal and the molecular model of the VL domain are practically identical. Although six amino acid residues had been replaced in the hypervariable regions, the CDR conformations remained conserved and only minor deviations in the orientation of some side-chains and peptide planes were detected. The crystallographic analysis of the VL domain modelled as part of a complex between an artificial Fv fragment and the small protein cystatin, deliberately chosen as antigen target, confirms the concept of distinct structural classes for CDR backbones and supports our strategy for the de novo design of an antibody combining site.
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<StructureSection load='1ivl' size='340' side='right'caption='[[1ivl]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1ivl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IVL FirstGlance]. <br>
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1IVL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct] with <scene name='pdbligand=IPA:'>IPA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IVL OCA].
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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]] 2.17&#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=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
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==Reference==
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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=1ivl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ivl OCA], [https://pdbe.org/1ivl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ivl RCSB], [https://www.ebi.ac.uk/pdbsum/1ivl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ivl ProSAT]</span></td></tr>
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The de novo design of an antibody combining site. Crystallographic analysis of the VL domain confirms the structural model., Essen LO, Skerra A, J Mol Biol. 1994 Apr 29;238(2):226-44. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8158652 8158652]
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</table>
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Synthetic construct]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Essen, L O.]]
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Check<jmol>
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[[Category: Skerra, A.]]
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<jmolCheckbox>
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[[Category: IPA]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/1ivl_consurf.spt"</scriptWhenChecked>
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[[Category: immunoglobulin]]
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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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:16:06 2008''
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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=1ivl ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Mus musculus]]
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[[Category: Essen L-O]]
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[[Category: Skerra A]]

Current revision

THE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHIC ANALYSIS OF THE VL DOMAIN CONFIRMS THE STRUCTURAL MODEL

PDB ID 1ivl

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