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Yorodumi- PDB-2k0u: High Resolution Solution NMR Structures of Oxaliplatin-DNA Adduct -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k0u | ||||||
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Title | High Resolution Solution NMR Structures of Oxaliplatin-DNA Adduct | ||||||
Components |
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Keywords | DNA / Oxaliplatin-DNA Adduct | ||||||
Function / homology | CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Bhattacharyya, D. / King, C.L. / Chaney, S.G. / Campbell, S.L. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links. Authors: Bhattacharyya, D. / Ramachandran, S. / Sharma, S. / Pathmasiri, W. / King, C.L. / Baskerville-Abraham, I. / Boysen, G. / Swenberg, J.A. / Campbell, S.L. / Dokholyan, N.V. / Chaney, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k0u.cif.gz | 26.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k0u.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 2k0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/2k0u ftp://data.pdbj.org/pub/pdb/validation_reports/k0/2k0u | HTTPS FTP |
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-Related structure data
Related structure data | 2k0tC 2k0vC 2k0w C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3565.316 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3761.468 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-1PT / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM mM Oxaliplatin-DNA Adduct, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1 mM / Component: Oxaliplatin-DNA Adduct |
Sample conditions | Ionic strength: 50 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 700 MHz |
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-Processing
NMR software | Name: CNS / Developer: Brunger A. T. et.al. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: energy based refinement with NOE distance constraints |
NMR representative | Selection criteria: minimized average structure |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 1 |
NMR ensemble rms | Bond angle rms dev: 0.695 ° / Covalent bond rms dev: 0.0021 Å / Dihedral angles rms dev: 1.859 ° / Improper torsion angle rms dev: 0.311 ° |