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Yorodumi- PDB-7nbk: Solution structure of DNA duplex containing a 2'-deoxy-2'2'-diflu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nbk | |||||||||||||||||||||||||||||||
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Title | Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Fluorine modification / modified DNA / gemcitabine | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / molecular dynamics | Authors | Cabrero, C. / Martin-Pintado, N. / Mazzini, S. / Gargallo, R. / Eritja, R. / Avino, A. / Gonzalez, C. | Funding support | Spain, 2items |
Citation | Journal: Chemistry / Year: 2021 | Title: Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes. Authors: Cabrero, C. / Martin-Pintado, N. / Mazzini, S. / Gargallo, R. / Eritja, R. / Avino, A. / Gonzalez, C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nbk.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nbk.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 7nbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nbk_validation.pdf.gz | 325.8 KB | Display | wwPDB validaton report |
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Full document | 7nbk_full_validation.pdf.gz | 377.1 KB | Display | |
Data in XML | 7nbk_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 7nbk_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/7nbk ftp://data.pdbj.org/pub/pdb/validation_reports/nb/7nbk | HTTPS FTP |
-Related structure data
Related structure data | 7nblC 7nejC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 1845.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 5 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |