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Yorodumi- PDB-2mnx: Major groove orientation of the (2S)-N6-(2-hydroxy-3-buten-1-yl)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mnx | ||||||
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Title | Major groove orientation of the (2S)-N6-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene | ||||||
Components |
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Keywords | DNA / B-form / 11-mer | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model1 | ||||||
Authors | Kowal, E.A. / Kotapati, S. / Turo, M. / Tretyakova, N. / Stone, M.P. | ||||||
Citation | Journal: Chem.Res.Toxicol. / Year: 2014 Title: Major Groove Orientation of the (2S)-N(6)-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA Adduct Induced by 1,2-Epoxy-3-butene. Authors: Kowal, E.A. / Wickramaratne, S. / Kotapati, S. / Turo, M. / Tretyakova, N. / 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 | 2mnx.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mnx.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 2mnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mnx_validation.pdf.gz | 333.4 KB | Display | wwPDB validaton report |
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Full document | 2mnx_full_validation.pdf.gz | 395.3 KB | Display | |
Data in XML | 2mnx_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 2mnx_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/2mnx ftp://data.pdbj.org/pub/pdb/validation_reports/mn/2mnx | HTTPS FTP |
-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: 3486.353 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3291.145 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 |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / 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 / NOE constraints total: 283 / NOE intraresidue total count: 125 / NOE sequential total count: 158 | ||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 9 / Conformers submitted total number: 9 |