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Yorodumi- PDB-2kf8: Structure of a two-G-tetrad basket-type intramolecular G-quadrupl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kf8 | ||||||
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Title | Structure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by human telomeric repeats in K+ solution | ||||||
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 / molecular dynamics | ||||||
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 | 2kf8.cif.gz | 149 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kf8.ent.gz | 129.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/2kf8 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/2kf8 | HTTPS FTP |
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-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: 6974.483 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 | pH: 7 / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: This natural sequence exhibits the same conformation as the 7BRG-substituted sequence, which has a much cleaner NMR spectrum. 10 relaxation matrix intensity-refined structures of the 7BRG ...Details: This natural sequence exhibits the same conformation as the 7BRG-substituted sequence, which has a much cleaner NMR spectrum. 10 relaxation matrix intensity-refined structures of the 7BRG form with the lowest energy were taken, the bromine atoms were replaced with hydrogen atoms, and the structures were subsequently subjected to distance-retrained molecular dynamics refinement. | ||||||||||||||||||||
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 / Hydrogen bond constraints total count: 42 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1 |