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Yorodumi- PDB-1d37: INFLUENCE OF AGLYCONE MODIFICATIONS ON THE BINDING OF ANTHRACYCLI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d37 | ||||||||||||||||||
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Title | INFLUENCE OF AGLYCONE MODIFICATIONS ON THE BINDING OF ANTHRACYCLINE DRUGS TO DNA: THE MOLECULAR STRUCTURE OF IDARUBICIN AND 4-O-DEMETHYL-11-DEOXYDOXORUBICIN COMPLEXED TO D(CGATCG) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 1-O-DEMETHYL-6-DEOXYDOXORUBICIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | Authors | Gao, Y.-G. / Wang, A.H.-J. | Citation | Journal: Anti-Cancer Drug Des. / Year: 1991 Title: Influence of aglycone modifications on the binding of anthracycline drugs to DNA: the molecular structure of idarubicin and 4-O-demethyl-11-deoxydoxorubicin complexed to d(CGATCG). Authors: Gao, Y.G. / Wang, A.H. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Facile Formation of Crosslinked Adduct between DNA and the Daunorubicin Derivative MAR70 Mediated by Formaldehyde: Molecular Structure of the MAR70-d(CGTnACG) Covalent Adduct Authors: Gao, Y.-G. / Liaw, Y.-C. / Li, Y.-K. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d37.cif.gz | 15.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d37.ent.gz | 8.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d37_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 1d37_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 1d37_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 1d37_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d37 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d37 | HTTPS FTP |
-Related structure data
-Links
-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-DM4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 298.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion / pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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. obs: 1247 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Observed criterion σ(F): 2 |
-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: 0.179 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.025 |