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Open data
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Basic information
Entry | Database: PDB / ID: 2mko | ||||||||||||||||||||
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Title | G-triplex structure and formation propensity | ||||||||||||||||||||
![]() | DNA_(5'-D(*![]() DNA / G-triplex / G-triad | Function / homology | : / DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / restrained molecular dynamics | Model details | closest to the average, model1 | ![]() Cerofolini, L. / Fragai, M. / Giachetti, A. / Limongelli, V. / Luchinat, C. / Novellino, E. / Parrinello, M. / Randazzo, A. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.8 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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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#2: Chemical | ChemComp-K / |
-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 / 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 sugar pucker constraints total count: 50 / Hydrogen bond constraints total count: 22 | |||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |