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Yorodumi- PDB-2mco: Structural studies on dinuclear ruthenium(II) complexes that bind... -
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-Basic information
Entry | Database: PDB / ID: 2mco | ||||||
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Title | Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an anti-parallel folded human telomere sequence | ||||||
Components | human telomere quadruplex | ||||||
Keywords | DNA / quadruplex / complex / ruthenium | ||||||
Function / homology | Chem-2FJ / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Williamson, M.P. / Wilson, T. / Thomas, J.A. / Felix, V. / Costa, P.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Structural Studies on Dinuclear Ruthenium(II) Complexes That Bind Diastereoselectively to an Antiparallel Folded Human Telomere Sequence. Authors: Wilson, T. / Costa, P.J. / Felix, V. / Williamson, M.P. / Thomas, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mco.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mco.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 2mco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mco_validation.pdf.gz | 536.8 KB | Display | wwPDB validaton report |
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Full document | 2mco_full_validation.pdf.gz | 653.6 KB | Display | |
Data in XML | 2mco_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 2mco_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/2mco ftp://data.pdbj.org/pub/pdb/validation_reports/mc/2mco | HTTPS FTP |
-Related structure data
Related structure data | 2mccC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: standard solid phase synthesis, hplc purified |
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#2: Chemical | ChemComp-2FJ / |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Complex of LL-[{Ru(bipy)2}2tppz]4+ bound to human telomere sequence quadruplex DNA (basket). Structures used NMR intermolecular restraints followed by unrestrained MD. The 5 structures in ...Details: Complex of LL-[{Ru(bipy)2}2tppz]4+ bound to human telomere sequence quadruplex DNA (basket). Structures used NMR intermolecular restraints followed by unrestrained MD. The 5 structures in the ensemble are representatives of the 5 most populated clusters from a 50 ns simulation. Simulation had explicit solvent plus counterions, which are removed in these files except for two sodiums in the middle of the quadruplex. | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.3 mM human telomere quadruplex, 0.3 mM LL-(Ru[bipy]2)tppz4+, 50 mM sodium chloride, 100% D2O Solvent system: 100% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR constraints | NOE constraints total: 13 / NOE intraresidue total count: 0 / NOE long range total count: 0 / NOE medium range total count: 0 / NOE sequential total count: 0 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 5 / Conformers submitted total number: 5 / Maximum lower distance constraint violation: 0.5 Å / Maximum upper distance constraint violation: 0.5 Å | ||||||||||||
NMR ensemble rms | Distance rms dev: 0.1 Å / Distance rms dev error: 0.05 Å |