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- PDB-7kbx: Solution structure of the major MYC promoter G-quadruplex in comp... -

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Basic information

Entry
Database: PDB / ID: 7kbx
TitleSolution structure of the major MYC promoter G-quadruplex in complex with NSC85697, a quinoline derivative
ComponentsMyc2345_T23
KeywordsDNA / G-QUADRUPLEX DNA / DRUG-DNA COMPLEX
Function / homologyChem-WAM / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsDickerhoff, J. / Yang, D.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA177585 United States
German Research Foundation (DFG)427347592 Germany
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes.
Authors: Dickerhoff, J. / Dai, J. / Yang, D.
History
DepositionOct 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myc2345_T23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6793
Polymers7,0091
Non-polymers6712
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Myc2345_T23


Mass: 7008.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-WAM / 2-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]-1-methyl-quinoline-4-carboxamide


Mass: 335.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N2O3 / 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 NOESY
221isotropic12D NOESY

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Sample preparation

DetailsType: solution
Contents: 0.7 mM Myc2345_T23, 2.1 mM NSC85697, 10 mM potassium phosphate, 90% H2O/10% D2O
Label: Myc2345_T23+85697 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMMyc2345_T23natural abundance1
2.1 mMNSC85697natural abundance1
10 mMpotassium phosphatenatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMconditions_16.51 atm298 K
210 mMconditions_26.51 atm293 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 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
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
Refinement
MethodSoftware ordinal
simulated annealing5
simulated annealing2
molecular dynamics1
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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