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- PDB-2k0t: High Resolution Solution NMR Structures of Oxaliplatin-DNA Adduct -
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Open data
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Basic information
Entry | Database: PDB / ID: 2k0t | ||||||
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Title | High Resolution Solution NMR Structures of Oxaliplatin-DNA Adduct | ||||||
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![]() | DNA / Oxaliplatin-DNA Adduct | ||||||
Function / homology | CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) / DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | High resolution solution NMR structures (ensemble) of Oxaliplatin-DNA adduct in a DNA dodecamer duplex | ||||||
![]() | Bhattacharyya, D. / King, C.L. / Chaney, S.G. / Campbell, S.L. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.5 KB | Display | ![]() |
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PDB format | ![]() | 168.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 383 KB | Display | ![]() |
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Full document | ![]() | 455.4 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2k0uC ![]() 2k0vC ![]() 2k0w C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Details: High resolution solution NMR structures (ensemble) of Oxaliplatin-DNA adduct in a DNA dodecamer duplex | ||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1 mM OXALIPLATIN-DNA ADDUCT, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1 mM Component: DNA (5'-D(*DGP*DGP*DAP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DGP*DG)-3') |
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: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 13 |
NMR ensemble rms | Bond angle rms dev: 0.703 ° / Covalent bond rms dev: 0.0021 Å / Dihedral angles rms dev: 1.854 ° / Improper torsion angle rms dev: 0.317 ° |