148d | pdb_0000148d

THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA APTAMER D(GGTTGGTGTGGTTGG)

spinqualitylabelsall models 148d Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 148d is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Solution NMR Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The DNA oligonucleotide d(GGTTGGTGTGGTTGG) (thrombin aptamer) binds to thrombin and inhibits its enzymatic activity in the chain of reactions that lead to blood clotting. Two-dimensional 1H NMR studies indicate that the oligonucleotide forms a folded structure in solution, composed of two guanine quartets connected by two T-T loops spanning the narrow grooves at one end and a T-G-T loop spanning a wide groove at the other end. We present the assignment strategy used, methods for the structure determination, and the refined three-dimensional structure of the thrombin aptamer. The initial structures were generated by metric matrix distance geometry using distance and dihedral bond angle constraints from NOE and coupling constants, respectively, and refined by restrained molecular dynamics and direct NOE refinement. Knowledge of the three-dimensional structure of this thrombin aptamer may be relevant for the design of improved thrombin-inhibiting anti-coagulants with similar structural motifs. Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG).,Schultze P, Macaya RF, Feigon J J Mol Biol. 1994 Feb 4;235(5):1532-47. PMID:8107090 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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