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Yorodumi- PDB-2n60: G-quadruplexes with (4n-1) guanines in the G-tetrad core: formati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n60 | ||||||||||||||||||||||
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Title | G-quadruplexes with (4n-1) guanines in the G-tetrad core: formation of a G-triad water complex and implication for small-molecule binding | ||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / Vacant site / 11 guanines / G-triad / K+ solution | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic (others) | Method | SOLUTION NMR / molecular dynamics, DGSA-distance geometry simulated annealing, simulated annealing | Model details | lowest energy, model1 | Authors | Heddi, B. / Martin-Pintado, N. / Serimbetov, Z. / Kari, T.M. / Phan, A.T. | Citation | Journal: Nucleic Acids Res. / Year: 2016 | Title: G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding Authors: Heddi, B. / Martin-Pintado, N. / Serimbetov, Z. / Kari, T.M. / Phan, A.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n60.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n60.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 2n60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/2n60 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/2n60 | 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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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 5705.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others) |
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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 | Ionic strength: 45 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics, DGSA-distance geometry simulated annealing, simulated annealing Software ordinal: 1 | |||||||||||||||||||||||||||||||||
NMR constraints | NA chi-angle constraints total count: 11 / NOE intraresidue total count: 91 / NOE medium range total count: 12 / NOE sequential total count: 45 | |||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Representative conformer: 1 |