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- PDB-1d22: BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d22 | ||||||||||||||||||
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Title | BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | U-58872, HYDROXY DERIVATIVE OF NOGALAMYCIN / DNA | ![]() Method | ![]() ![]() Gao, Y.-G. / Liaw, Y.-C. / Robinson, H. / Wang, A.H.-J. | ![]() ![]() Title: Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison. Authors: Gao, Y.G. / Liaw, Y.C. / Robinson, H. / Wang, A.H. #1: ![]() Title: NMR Studies on the Binding of Antitumor Drug Nogalamycin to DNA Hexamer d(CGTACG) Authors: Robinson, H. / Liaw, Y.-C. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. #2: ![]() 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.-J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.5 KB | Display | ![]() |
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PDB format | ![]() | 15.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.2 KB | Display | ![]() |
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Full document | ![]() | 497.4 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 1853.336 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, temperature 298.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. all: 4210 / Num. obs: 2143 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.8 Å |
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Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 1.8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / σ(F): 2 / Rfactor obs: 0.196 / Num. reflection obs: 2143 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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