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- PDB-7csk: A 2:1 stoichiometric complex of anticancer drug Adriamycin bound ... -

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Basic information

Entry
Database: PDB / ID: 7csk
TitleA 2:1 stoichiometric complex of anticancer drug Adriamycin bound to parallel G-quadruplex DNA [d-(TTGGGGT)]4.
ComponentsDNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
KeywordsDNA / G-Quadruplex / Parallel stranded G-Quadruplex / Adriamycin / DNA-Drug Complex
Function / homologyDOXORUBICIN / DNA
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsBarthwal, R. / Tariq, Z. / Pandav, K.
CitationJournal: To Be Published
Title: A 2:1 stoichiometric complex of anticancer drug Adriamycin bound to parallel G-quadruplex DNA [d-(TTGGGGT)]4.
Authors: Barthwal, R. / Tariq, Z. / Pandav, K.
History
DepositionAug 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
B: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
C: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
D: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8256
Polymers8,7384
Non-polymers1,0872
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5070 Å2
ΔGint-26 kcal/mol
Surface area4470 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain
DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')


Mass: 2184.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29NO11 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic11D 1H

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Sample preparation

DetailsType: solution
Contents: 1.15 mM DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3'), 2.30 mM Adriamycin, 90% H2O/10% D2O
Label: 1H / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.15 mMDNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')natural abundance1
2.30 mMAdriamycinnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
TopSpin3.6.1Bruker Biospinchemical shift assignment
TopSpin3.6.1Bruker Biospinpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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