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Yorodumi- PDB-2le6: Structure of a dimeric all-parallel-stranded G-quadruplex stacked... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2le6 | ||||||||||||||||||||
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Title | Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / HIV-1 integrase inhibition / G-quadruplex / anticancer / stacking | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, distance-restrained molecular dynamics refinement in vacuo, distance-restrained molecular dynamics refinement in explicit solvent | Model details | lowest energy, model 1 | Authors | Do, N.Q. / Lim, K.W. / Teo, M.H. / Heddi, B. / Phan, A.T. | Citation | Journal: Nucleic Acids Res. / Year: 2011 | Title: Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity Authors: Do, N.Q. / Lim, K.W. / Teo, M.H. / Heddi, B. / Phan, A.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2le6.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2le6.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 2le6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2le6_validation.pdf.gz | 408.6 KB | Display | wwPDB validaton report |
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Full document | 2le6_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 2le6_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2le6_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/2le6 ftp://data.pdbj.org/pub/pdb/validation_reports/le/2le6 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 5107.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 100mM K+ / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, distance-restrained molecular dynamics refinement in vacuo, distance-restrained molecular dynamics refinement in explicit solvent 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: 10 / Representative conformer: 1 |