1keg | pdb_00001keg

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

spinqualitylabelsall models 1keg, resolution 2.40Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1keg is a 3 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.4Å Ligands: 64T, NI Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Monoclonal Antibodies 3D structures

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