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- PDB-1d11: INTERACTIONS BETWEEN AN ANTHRACYCLINE ANTIBIOTIC AND DNA MOLECULA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d11 | ||||||||||||||||||
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Title | INTERACTIONS BETWEEN AN ANTHRACYCLINE ANTIBIOTIC AND DNA MOLECULAR STRUCTURE OF DAUNOMYCIN COMPLEXED TO D(CPGPTPAPCPG) AT 1.2-ANGSTROMS RESOLUTION | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | DAUNOMYCIN / DNA | ![]() Method | ![]() ![]() Wang, A.H.-J. / Ughetto, G. / Quigley, G.J. / Rich, A. | ![]() ![]() Title: Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-A resolution. Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Rich, A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 17.2 KB | Display | ![]() |
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PDB format | ![]() | 9.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.1 KB | Display | ![]() |
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Full document | ![]() | 421.8 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-DM1 / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 / Method: other | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS Crystal-ID: 1
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-Data collection
Diffraction | Mean temperature: 288 K |
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Detector | Type: NICOLET P3X / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.2 Å / Num. all: 13258 / Num. obs: 9238 / Observed criterion σ(F): 2 |
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Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.18→10 Å / σ(F): 3 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.18→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.2 Å / Num. reflection obs: 5133 / σ(F): 3 / Rfactor obs: 0.175 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d |