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Yorodumi- PDB-2n4m: Base-displaced intercalated structure of the N-(2'deoxyguanosin-8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n4m | ||||||
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Title | Base-displaced intercalated structure of the N-(2'deoxyguanosin-8-yl)-3-aminobenzanthrone DNA adduct | ||||||
Components |
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Keywords | DNA | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | fewest violations, model1 | ||||||
Authors | Politica, D.A. / Stone, M.P. / Malik, C.K. / Basu, A.K. | ||||||
Citation | Journal: Chem.Res.Toxicol. / Year: 2015 Title: Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct. Authors: Politica, D.A. / Malik, C.K. / Basu, A.K. / Stone, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n4m.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n4m.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 2n4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/2n4m ftp://data.pdbj.org/pub/pdb/validation_reports/n4/2n4m | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3958.670 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3609.398 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-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: 900 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 18 / NA beta-angle constraints total count: 18 / NA delta-angle constraints total count: 18 / NA epsilon-angle constraints total count: 18 / NA gamma-angle constraints total count: 18 / NA sugar pucker constraints total count: 75 / NOE constraints total: 330 / NOE intraresidue total count: 171 / NOE sequential total count: 125 | ||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 85 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.083 Å / Maximum torsion angle constraint violation: 8.553 ° / Maximum upper distance constraint violation: 0.104 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0125 Å |