+Open data
-Basic information
Entry | Database: PDB / ID: 2mko | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2mko.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2mko.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 2mko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/2mko ftp://data.pdbj.org/pub/pdb/validation_reports/mk/2mko | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 3476.254 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Chemical | ChemComp-K / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-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 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||||||||
Sample conditions | Ionic strength: 0.08 / pH: 7 / Pressure: ambient / Temperature: 274 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |