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- PDB-6o2l: NMR structure of the 2:1 complex of a carbazole derivative BMVC b... -

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Basic information

Entry
Database: PDB / ID: 6o2l
TitleNMR structure of the 2:1 complex of a carbazole derivative BMVC bound to c-MYC G-quadruplex
ComponentsDNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3')
KeywordsDNA / G-quadruplex DNA / drug-DNA complex / BMVC
Function / homologyChem-BO6 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsLin, C. / Liu, W. / Yang, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA177585 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA023168 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition.
Authors: Liu, W. / Lin, C. / Wu, G. / Dai, J. / Chang, T.C. / Yang, D.
History
DepositionFeb 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8163
Polymers7,0091
Non-polymers8072
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3')


Mass: 7008.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-BO6 / 3,6-bis[(E)-2-(1-methylpyridin-1-ium-4-yl)ethenyl]-9H-carbazole


Mass: 403.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H25N3

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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
121isotropic12D DQF-COSY
131isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 2 mM DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'), 3 mM BMVC, 25 mM potassium phosphate, 70 mM potassium chloride, 90% H2O/10% D2O
Details: 100mM potassium phosphate buffer; 90% H2O, 10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMDNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3')natural abundance1
3 mMBMVCnatural abundance1
25 mMpotassium phosphatenatural abundance1
70 mMpotassium chloridenatural abundance1
Sample conditionsDetails: 100mM potassium phosphate buffer; 90% H2O, 10% D2O / Ionic strength: 100 mM / Label: 25C / pH: 7 / Pressure: 1 atm / Temperature: 298 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
NameDeveloperClassification
X-PLORBrungerrefinement
Insight IIAccelrys Software Inc.refinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Insight IIAccelrys Software Inc.structure calculation
Refinement
MethodSoftware ordinalDetails
simulated annealing1DGSA-distance geometry simulated annealing
molecular dynamics2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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