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Yorodumi- PDB-2kf7: Structure of a two-G-tetrad basket-type intramolecular G-quadrupl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kf7 | ||||||
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Title | Structure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by human telomeric repeats in K+ solution (with G7-to-BRG substitution) | ||||||
Components | HUMAN TELOMERE DNA | ||||||
Keywords | DNA / anticancer targets / human telomere / intramolecular G-quadruplexes | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / matrix relaxation, molecular dynamics, DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Lim, K.W. / Amrane, S. / Bouaziz, S. / Xu, W. / Mu, Y. / Patel, D.J. / Luu, K.N. / Phan, A.T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers Authors: Lim, K.W. / Amrane, S. / Bouaziz, S. / Xu, W. / Mu, Y. / Patel, D.J. / Luu, K.N. / 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 | 2kf7.cif.gz | 155.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kf7.ent.gz | 127.6 KB | Display | PDB format |
PDBx/mmJSON format | 2kf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kf7_validation.pdf.gz | 315.3 KB | Display | wwPDB validaton report |
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Full document | 2kf7_full_validation.pdf.gz | 373 KB | Display | |
Data in XML | 2kf7_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 2kf7_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/2kf7 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/2kf7 | HTTPS FTP |
-Related 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: 7053.379 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 |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: matrix relaxation, molecular dynamics, DGSA-distance geometry simulated annealing 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: 8 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 4 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 8 / NA sugar pucker constraints total count: 0 / NOE constraints total: 580 / NOE intraresidue total count: 272 / NOE long range total count: 40 / NOE medium range total count: 49 / NOE sequential total count: 219 / Hydrogen bond constraints total count: 42 | ||||||||||||||||||||
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: 0.193 Å / Maximum upper distance constraint violation: 0.239 Å / Representative conformer: 1 | ||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.018 Å / Distance rms dev error: 0.002 Å |