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Yorodumi- PDB-2km3: Structure of an intramolecular G-quadruplex containing a G.C.G.C ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2km3 | ||||||||||||||||||||
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Title | Structure of an intramolecular G-quadruplex containing a G.C.G.C tetrad formed by human telomeric variant CTAGGG repeats | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / anticancer targets / CTAGGG repeat / G-quadruplex / human telomere instability | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics, matrix relaxation | Model details | lowest energy, model 1 | Authors | Lim, K.W. / Alberti, P. / Guedin, A. / Lacroix, L. / Riou, J.F. / Royle, N.J. / Mergny, J.L. / Phan, A.T. | Citation | Journal: Nucleic Acids Res. / Year: 2009 | Title: Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G.C.G.C tetrad Authors: Lim, K.W. / Alberti, P. / Guedin, A. / Lacroix, L. / Riou, J.F. / Royle, N.J. / Mergny, J.L. / 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 | 2km3.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2km3.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 2km3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2km3_validation.pdf.gz | 308.1 KB | Display | wwPDB validaton report |
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Full document | 2km3_full_validation.pdf.gz | 361.6 KB | Display | |
Data in XML | 2km3_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 2km3_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/2km3 ftp://data.pdbj.org/pub/pdb/validation_reports/km/2km3 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6938.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis |
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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: 90mM 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, molecular dynamics, matrix relaxation Software ordinal: 1 | ||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 0 / NA beta-angle constraints total count: 0 / NA chi-angle constraints total count: 13 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 8 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 520 / NOE intraresidue total count: 208 / NOE long range total count: 49 / NOE medium range total count: 57 / NOE sequential total count: 208 / Hydrogen bond constraints total count: 50 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.177 Å / Maximum upper distance constraint violation: 0.216 Å / Representative conformer: 1 | ||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.019 Å / Distance rms dev error: 0.002 Å |