- PDB-170d: SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLAS... -
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データベース: PDB / ID: 170d
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SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT
手法: MOLECULAR DYNAMICS, MATRIX RELAXATION / ソフトェア番号: 1 詳細: STRUCTURES WERE GENERATED IN THE FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED FROM NOESY AND COSY NMR DATA. THREE ...詳細: STRUCTURES WERE GENERATED IN THE FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED FROM NOESY AND COSY NMR DATA. THREE STRUCTURES WERE GENERATED STARTING FROM CANONICAL A-TYPE DNA AND THREE STRUCTURES STARTING FROM CANONICAL B-TYPE DNA. FOR BOTH CONTROL AND ARAC STRUCTURES, THE RMSD OF THE SIX STRUCTURES WAS < 0.7 ANGSTROM. THE SIX STRUCTURES WERE AVERAGED, MINIMIZED AND REFINED USING RELAXATION MATRIX REFINEMENT IN A DYNAMICAL SIMULATED ANNEALING PROTOCOL. THE X-PLOR DISTANCE CONSTRAINT AND SUGAR DIHEDRAL CONSTRAINT TABLES USED IN THE RESTRAINED MOLECULAR DYNAMICS CALCULATIONS FOR THE ARAC-CONTAINING DODECAMER ARE AVAILABLE FROM THE PROTEIN DATA BANK AS A SEPARATE ENTRY.