+Open data
-Basic information
Entry | Database: PDB / ID: 2mkm | ||||||||||||||||||||
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Title | G-triplex structure and formation propensity | ||||||||||||||||||||
Components | DNA_(5'-D(*Keywords | DNA / G-triplex / G-triad | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / restrained Molecular Dynamics (rMD) | Model details | closest to the average, model1 | Authors | Cerofolini, L. / Fragai, M. / Giachetti, A. / Limongelli, V. / Luchinat, C. / Novellino, E. / Parrinello, M. / Randazzo, A. | Citation | Journal: Nucleic Acids Res. / Year: 2014 | Title: G-triplex structure and formation propensity. Authors: Cerofolini, L. / Amato, J. / Giachetti, A. / Limongelli, V. / Novellino, E. / Parrinello, M. / Fragai, M. / Randazzo, A. / Luchinat, C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mkm.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mkm.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 2mkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/2mkm ftp://data.pdbj.org/pub/pdb/validation_reports/mk/2mkm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3476.254 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.7 mM DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3'), 70 mM potassium chloride, 10 mM potassium phosphate, 0.2 mM EDTA, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.08 / pH: 7 / Pressure: ambient / Temperature: 274 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained Molecular Dynamics (rMD) / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NA beta-angle constraints total count: 6 / NA chi-angle constraints total count: 11 / NA gamma-angle constraints total count: 9 / NA other-angle constraints total count: 11 / NA sugar pucker constraints total count: 30 / Hydrogen bond constraints total count: 22 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 10 |