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- PDB-2llj: Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch -
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Open data
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Basic information
Entry | Database: PDB / ID: 2llj | ||||||
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Title | Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch | ||||||
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![]() | DNA / DNA thymine mismatch / macrocyle / bisintercalation | ||||||
Function / homology | Chem-LLJ / DNA / DNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Jourdan, M. / Granzhan, A. / Guillot, R. / Dumy, P. / Teulade-Fichou, M. | ||||||
![]() | ![]() Title: Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch. Authors: Jourdan, M. / Granzhan, A. / Guillot, R. / Dumy, P. / Teulade-Fichou, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.2 KB | Display | ![]() |
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PDB format | ![]() | 72.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 490.5 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 12.4 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: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-LLJ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1.5 mM DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3'), 1.5 mM DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3'), 1.5 mM 2,7-bisnaphthalene, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.06 / pH: 6 / Pressure: ambient / Temperature: 283 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 | ||||||||||||
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: 5 |