1ehl
From Proteopedia
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64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T
Overview
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.
About this Structure
1EHL is a Protein complex structure of sequences from Mus musculus. Full crystallographic information is available from OCA.
Reference
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:10835279
Page seeded by OCA on Sun Nov 18 09:29:12 2007
