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1ehl

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(New page: 200px<br /> <applet load="1ehl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ehl, resolution 2.4&Aring;" /> '''64M-2 ANTIBODY FAB C...)
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[[Image:1ehl.gif|left|200px]]<br />
 
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<applet load="1ehl" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ehl, resolution 2.4&Aring;" />
 
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'''64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T'''<br />
 
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==Overview==
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==64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T==
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DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by, ultraviolet radiation are implicated in mutagenesis and cancer, particularly skin cancer. The crystal structure of the Fab fragment of the, murine 64M-2 antibody specific to DNA T(6-4)T photoproducts is determined, as a complex with dT(6-4)T, a (6-4) pyrimidine-pyrimidone photodimer of, dTpT, at 2.4 A resolution to a crystallographic R-factor of 0.199 and an, R(free) value of 0.279. The 64M-2 Fab molecule is in an extended, arrangement with an elbow angle of 174 degrees, and its five, complementarity-determining regions, except L2, are involved in the ligand, binding. The bound dT(6-4)T ligand adopting a ring structure with (6-4), linked 5' thymine-3' pyrimidone bases is fully accommodated in an, antigen-binding pocket of about 15 Ax10 A. The 5'-thymine and, 3'-pyrimidone bases are in half-chair and planar conformations, respectively, and are nearly perpendicular to each other. The 5'-thymine, base is hydrogen-bonded to Arg95H and Ser96H, and is in van der Waals, contact with Tyr100iH. The 3'-pyrimidone base is hydrogen-bonded to, His35H, and is in contact with Trp33H. Three water molecules are located, at the interface between the bases and the Fab residues. Hydrogen bonds, involving these water molecules also contribute to Fab recognition of the, dT(6-4)T bases. The sugar-phosphate backbone connecting the bases is, surrounded by residues His27dL, Tyr32L, Ser92L, Trp33H, and Ser58H, but is, not hydrogen-bonded to these residues.
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<StructureSection load='1ehl' size='340' side='right'caption='[[1ehl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ehl]] is a 3 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=1EHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EHL 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]] 2.4&#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=5HT:5-HYDROXY-THYMIDINE'>5HT</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=1ehl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ehl OCA], [https://pdbe.org/1ehl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ehl RCSB], [https://www.ebi.ac.uk/pdbsum/1ehl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ehl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IGKC_MOUSE IGKC_MOUSE]
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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/eh/1ehl_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=1ehl ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1EHL is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EHL OCA].
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*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation., Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O, J Mol Biol. 2000 Jun 9;299(3):711-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10835279 10835279]
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Protein complex]]
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[[Category: Komatsu Y]]
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[[Category: Komatsu, Y.]]
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[[Category: Mizutani R]]
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[[Category: Mizutani, R.]]
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[[Category: Nikaido O]]
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[[Category: Nikaido, O.]]
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[[Category: Ohtsuka E]]
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[[Category: Ohtsuka, E.]]
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[[Category: Satow Y]]
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[[Category: Satow, Y.]]
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[[Category: Yokoyama H]]
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[[Category: Yokoyama, H.]]
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[[Category: dna photoproduct]]
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[[Category: immunoglobulin]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:29:12 2007''
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Current revision

64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T

PDB ID 1ehl

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