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Open data
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Basic information
Entry | Database: PDB / ID: 6jwd | ||||||||||||||||||||
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Title | structure of RET G-quadruplex in complex with berberine | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / RET / G-quadruplex / berberine | Function / homology | BERBERINE / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | SOLUTION NMR / simulated annealing | ![]() Wang, F. / Wang, C. / Liu, Y. / Lan, W.X. / Li, Y.M. / Wang, R.X. / Cao, 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 | ![]() | 265.8 KB | Display | ![]() |
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PDB format | ![]() | 222.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.3 KB | Display | ![]() |
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Full document | ![]() | 591.9 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jweC C: citing same article ( |
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Similar structure data | |
Other databases |
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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: 6394.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Chemical | ChemComp-BER / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 1.4 mM RET G4-DNA, 1.68 mM BERBERINE, 20 mM Potassium Phosphate Monobasic, 80 mM potassium chloride, 90% H2O/10% D2O Label: RET G4-DNA sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: RET G4 berberine solution complex / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |