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- PDB-7z9l: Phen-DC3 intercalation causes hybrid-to-antiparallel transformati... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z9l | ||||||||||||||||||||||||||||||||||||||||
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Title | Phen-DC3 intercalation causes hybrid-to-antiparallel transformation of human telomeric DNA G-quadruplex | ||||||||||||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / G Quadruplex / ligand intercalation / NMR spectroscopy / Mass spectrometry | Function / homology | Chem-PQ3 / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | SOLUTION NMR / simulated annealing | ![]() Ghosh, A. / Trajkovski, M. / Teulade-Fichou, M.P. / Gabelica, V. / Plavec, J. | Funding support | European Union, | ![]() ![]()
![]() ![]() Title: Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation. Authors: Ghosh, A. / Trajkovski, M. / Teulade-Fichou, M.P. / Gabelica, V. / Plavec, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.8 KB | Display | ![]() |
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PDB format | ![]() | 133.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 494.9 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 7287.690 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The DNA is bound to a small molecule named N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide(Phen-DC3). Three letter code (PQ3). Source: (synth.) ![]() |
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#2: Chemical | ChemComp-PQ3 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions | Details: 20 mM KCl, 70 mM potassium phosphate buffer with pH 7.0 containing 95% H2O+ 5% D2O and 100% D2O Ionic strength: 70 mM Label: 20 mM KCl, 70 mM potassium phosphate buffer with pH 7.0 containing 5% D2O pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: 497 distance, 24 Planarity, 23 dihedral angle, 16 H bonding | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |