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Yorodumi- PDB-1d35: FACILE FORMATION OF A CROSSLINKED ADDUCT BETWEEN DNA AND THE DAUN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d35 | ||||||||||||||||||
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Title | FACILE FORMATION OF A CROSSLINKED ADDUCT BETWEEN DNA AND THE DAUNORUBICIN DERIVATIVE MAR70 MEDIATED BY FORMALDEHYDE: MOLECULAR STRUCTURE OF THE MAR70-D(CGTNACG) COVALENT ADDUC | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | 4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.3 Å | Authors | Gao, Y.-G. / Liaw, Y.-C. / Li, Y.-K. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Facile formation of a 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. #1: 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.-J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d35.cif.gz | 17 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d35.ent.gz | 9.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d35_validation.pdf.gz | 417.2 KB | Display | wwPDB validaton report |
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Full document | 1d35_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 1d35_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 1d35_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d35 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d35 | 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: 1838.258 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-MAR / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 295.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.3 Å / Num. obs: 2599 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.3 Å / Observed criterion σ(F): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||
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Refinement | Highest resolution: 1.3 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 1.3 Å
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Refinement | *PLUS Highest resolution: 1.3 Å / Rfactor obs: 0.174 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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