1keg

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[[Image:1keg.gif|left|200px]]
 
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{{Structure
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==Antibody 64M-2 Fab complexed with dTT(6-4)TT==
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|PDB= 1keg |SIZE=350|CAPTION= <scene name='initialview01'>1keg</scene>, resolution 2.40&Aring;
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<StructureSection load='1keg' size='340' side='right'caption='[[1keg]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NI:NICKEL (II) ION'>NI</scene>
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<table><tr><td colspan='2'>[[1keg]] 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=1KEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEG FirstGlance]. <br>
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|ACTIVITY=
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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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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=64T:5-HYDROXY-THYMIDINE-5-MONOPHOSPHATE'>64T</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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}}
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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=1keg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1keg OCA], [https://pdbe.org/1keg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1keg RCSB], [https://www.ebi.ac.uk/pdbsum/1keg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1keg ProSAT]</span></td></tr>
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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/ke/1keg_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1keg 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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Pyrimidine (6-4) pyrimidone DNA photoproducts produced by ultraviolet light are highly mutagenic and carcinogenic. The crystal structure of the dTT(6-4)TT photoproduct in complex with the Fab fragment of the antibody 64M-2 that is specific for (6-4) photoproducts was determined at 2.4 A resolution. The dT(6-4)T segment is fully accommodated in the concave binding pocket of the Fab, as observed in the complex of dT(6-4)T with the Fab. The pyrimidine and pyrimidone bases of the dT(6-4)T segment are positioned nearly perpendicularly to each other. The thymidine segments flanking both ends extend away from the dT(6-4)T segment. The 5'-side thymine base is parallel to the side chain of Tyr100iH of the antibody heavy chain and is also involved in electrostatic interactions with Asn30L, Tyr32L and Lys50L of the antibody light chain. The 5'-side and 3'-side phosphate groups exhibit electrostatic interactions with Asn28L and Ser58H, respectively. These interactions with the flanking nucleotides explain why longer oligonucleotides containing dT(6-4)T segments in the centre show higher antibody-binding affinities than the dT(6-4)T ligand.
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'''Antibody 64M-2 Fab complexed with dTT(6-4)TT'''
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Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides.,Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):232-8. Epub 2012 Feb 7. PMID:22349224<ref>PMID:22349224</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1keg" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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1KEG is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEG OCA].
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*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 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]]
[[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: Sato K]]
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[[Category: Sato, K.]]
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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: NI]]
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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://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:16:19 2008''
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Current revision

Antibody 64M-2 Fab complexed with dTT(6-4)TT

PDB ID 1keg

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