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1fvd

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[[Image:1fvd.gif|left|200px]]
 
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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 line below this paragraph, containing "STRUCTURE_1fvd", creates the "Structure Box" on the page.
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<StructureSection load='1fvd' size='340' side='right'caption='[[1fvd]], [[Resolution|resolution]] 2.50&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'>[[1fvd]] 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=1FVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FVD 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]] 2.5&#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=1fvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fvd OCA], [https://pdbe.org/1fvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fvd RCSB], [https://www.ebi.ac.uk/pdbsum/1fvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fvd ProSAT]</span></td></tr>
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{{STRUCTURE_1fvd| PDB=1fvd | SCENE= }}
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</table>
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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/fv/1fvd_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=1fvd ConSurf].
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<div style="clear:both"></div>
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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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==See Also==
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[Sandbox 20009|Sandbox 20009]]
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==Overview==
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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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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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Homo sapiens]]
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1FVD is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FVD OCA].
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[[Category: Large Structures]]
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[[Category: Eigenbrot C]]
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==Reference==
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[[Category: Kossiakoff AA]]
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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://www.ncbi.nlm.nih.gov/pubmed/8095303 8095303]
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[[Category: Presta L]]
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[[Category: Protein complex]]
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[[Category: Randal M]]
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[[Category: Eigenbrot, C.]]
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[[Category: Kossiakoff, A A.]]
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[[Category: Presta, L.]]
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[[Category: Randal, M.]]
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[[Category: Immunoglobulin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 16:48:22 2008''
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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 1fvd

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