+Open data
-Basic information
Entry | Database: PDB / ID: 202d | ||||||||||||||||||
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Title | SOLUTION STRUCTURE OF THE MENOGARIL-DNA COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / MENOGARIL | Function / homology | MENOGARIL / DNA | Function and homology information Method | SOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | Authors | Chen, H. / Patel, D.J. | Citation | Journal: J.Am.Chem.Soc. / Year: 1995 Title: Solution Structure of the Menogaril-DNA Complex Authors: Chen, H. / Patel, D.J. #1: Journal: Biochemistry / Year: 1989 Title: Antitumor Drug Nogalamycin Binds DNA in Both Grooves Simultaneously: Molecular Structure of Nogalamycin-DNA Complex Authors: Liaw, Y.-C. / Gao, Y.-G. / Robinson, H. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 202d.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb202d.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 202d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/02/202d ftp://data.pdbj.org/pub/pdb/validation_reports/02/202d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: MENOGARIL WAS PROVIDED BY UPJOHN CO., KALAMAZOO, MICHIGAN. |
-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Refinement | Method: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1 Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A ...Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 100, 150 AND 200 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.039 0.038 0.038 0.036 BOND (ANG) 0.012 0.012 0.012 0.011 ANGLES (DEG) 3.833 3.818 3.776 3.684 IMPROPERS (DEG) 0.251 0.250 0.286 0.219 |
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NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 4 / Conformers submitted total number: 4 |