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1fvc

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(New page: 200px<br /> <applet load="1fvc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fvc, resolution 2.2&Aring;" /> '''X-RAY STRUCTURES OF ...)
Current revision (11:16, 27 March 2024) (edit) (undo)
 
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[[Image:1fvc.gif|left|200px]]<br />
 
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<applet load="1fvc" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1fvc, resolution 2.2&Aring;" />
 
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'''X-RAY STRUCTURES OF THE ANTIGEN-BINDING DOMAINS FROM THREE VARIANTS OF HUMANIZED ANTI-P185-HER2 ANTIBODY 4D5 AND COMPARISON WITH MOLECULAR MODELING'''<br />
 
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==Overview==
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==X-RAY STRUCTURES OF THE ANTIGEN-BINDING DOMAINS FROM THREE VARIANTS OF HUMANIZED ANTI-P185-HER2 ANTIBODY 4D5 AND COMPARISON WITH MOLECULAR MODELING==
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The X-ray structures of 1 Fv and 2 Fab humanized anti-p185HER2 antibody, fragments (IgG1-kappa) have been determined at a resolution between 2.7 A, and 2.2 A. The antibodies are three different versions of a human antibody, framework onto which the antigen recognition loops from a murine antibody, (4D5) have been grafted. The sequences of the three versions differ in the, framework region at positions L55, H78 and H102. The version 8 Fv fragment, crystallizes in space group P2(1) with cell parameters a = 37.6 A, b =, 63.4 A, c = 90.2 A, beta = 98.2 degrees, with two molecules per asymmetric, unit, and has been refined against data 10.0 A-2.2 A to an R-factor of, 18.3%. Versions 4 and 7 Fabs crystallize in space group P1 with cell, parameters a = 39.2 A, b = 80.2 A, c = 86.1 A, alpha = 113.1 degrees, beta, = 92.7 A, gamma = 102.6 A and two molecules per asymmetric unit. Version 4, has been refined against data 10.0 A-2.5 A resolution to an R-factor of, 17.9%. Version 7 has been refined against data 10 A-2.7 A to an R-factor, of 17.1%. The X-ray structures have been used to assess the accuracy of, structural predictions made via molecular modeling, and they confirm the, structural role of certain framework residues and the conformations of, five of six complementarity determining regions (CDRS). The average, deviation of the model from the X-ray structures is within the range, observed among the X-ray structures for 81% of the C alpha atoms. Of the, hydrogen bonds common to the X-ray structures, 94% of the, main-chain-main-chain and 79% of the main-chain-side-chain ones were, predicted by the model. The side-chain conformation was predicted, correctly for 79% of the buried residues. The third CDR in the heavy chain, is variable, differing by up to 8 A between molecules within an asymmetric, unit. The structural relationship between variable domains of light and, heavy chains is not significantly altered by the absence of constant, domains in the Fv molecule. The antigen-binding potential of an unusual, light chain sequence has been confirmed. The arginine at position 66, interacts with the first light chain CDR, but in a fashion somewhat, different than predicted. A substitution of a leucine for an alanine, side-chain directed between the beta-sheets has only relatively small and, local effects.(ABSTRACT TRUNCATED AT 400 WORDS)
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<StructureSection load='1fvc' size='340' side='right'caption='[[1fvc]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1fvc]] is a 4 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=1FVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FVC FirstGlance]. <br>
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1FVC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FVC 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]] 2.2&#8491;</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=1fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fvc OCA], [https://pdbe.org/1fvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fvc RCSB], [https://www.ebi.ac.uk/pdbsum/1fvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fvc ProSAT]</span></td></tr>
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==Reference==
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</table>
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X-ray structures of the antigen-binding domains from three variants of humanized anti-p185HER2 antibody 4D5 and comparison with molecular modeling., Eigenbrot C, Randal M, Presta L, Carter P, Kossiakoff AA, J Mol Biol. 1993 Feb 20;229(4):969-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8095303 8095303]
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== Evolutionary Conservation ==
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[[Category: Single protein]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Eigenbrot, C.]]
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Check<jmol>
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[[Category: Kossiakoff, A.A.]]
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<jmolCheckbox>
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[[Category: Presta, L.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fv/1fvc_consurf.spt"</scriptWhenChecked>
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[[Category: Randal, M.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: immunoglobulin]]
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:30:43 2007''
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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=1fvc 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: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Eigenbrot C]]
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[[Category: Kossiakoff AA]]
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[[Category: Presta L]]
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[[Category: Randal M]]

Current revision

X-RAY STRUCTURES OF THE ANTIGEN-BINDING DOMAINS FROM THREE VARIANTS OF HUMANIZED ANTI-P185-HER2 ANTIBODY 4D5 AND COMPARISON WITH MOLECULAR MODELING

PDB ID 1fvc

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