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- PDB-1nab: The crystal structure of the complex between a disaccharide anthr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nab | ||||||||||||||||||
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Title | The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / right handed dna / double helix / complexed with drug | Function / homology | Chem-44D / DNA | ![]() Method | ![]() ![]() ![]() ![]() Temperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G. | ![]() ![]() Title: The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes Authors: Temperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G. #1: ![]() Title: Structural comparison of anticancer drug-dna complexes: adriamycin and daunomycin Authors: Frederick, C.A. / Williams, L.D. / Ughetto, G. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.3 KB | Display | ![]() |
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PDB format | ![]() | 13.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 991.2 KB | Display | ![]() |
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Full document | ![]() | 1017.9 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 8.7 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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Unit cell |
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Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: automatic synthesis #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium chloride, cacodylate, spermine hydrochloride, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 27, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→18.9 Å / Num. all: 28812 / Num. obs: 28737 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.0874 / % possible all: 75.6 |
Reflection | *PLUS Lowest resolution: 8 Å / Num. obs: 2621 |
Reflection shell | *PLUS Highest resolution: 2.15 Å / % possible obs: 75.6 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.37 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.2 Å /
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Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.15 Å / Lowest resolution: 2.17 Å |