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- PDB-8abn: Solution structure of a phenyl-indoloquinoline intercalating into... -

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Basic information

Entry
Database: PDB / ID: 8abn
TitleSolution structure of a phenyl-indoloquinoline intercalating into a quadruplex-duplex hybrid
ComponentsDNA (27-MER)
KeywordsDNA / G-quadruplex / Duplex / Quadruplex-Duplex Junction / Indoloquinoline / Intercalation
Function / homologyChem-LNF / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsVianney, Y.M. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)410497337 Germany
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.
Authors: Vianney, Y.M. / Weisz, K.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 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 (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9402
Polymers8,4451
Non-polymers4951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area400 Å2
ΔGint4 kcal/mol
Surface area5440 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (27-MER)


Mass: 8445.403 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The first residue is a guanosine, however, the H1 is at the N1, not at the N3.
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LNF / diethyl-[3-[[4-(4,5,9-trimethyl-10H-indolo[3,2-b]quinolin-5-ium-11-yl)phenyl]carbonylamino]propyl]azanium / 4,N5,9-Trimethyl-11-(4-((3-diethylaminopropyl)carbamoyl)phenyl-10H-indolo[3,2-b]quinolinium


Mass: 494.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H38N4O
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
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 0.64 mM no PIQ-QD2l, 90% H2O/10% D2O / Details: 120 mM Potassium phosphate buffer, pH 7.0 / Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.64 mM / Component: PIQ-QD2l / Isotopic labeling: no
Sample conditionsIonic strength: 120 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIH3.0.3Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
TopSpin4.0.7Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNdata analysis
CcpNmr Analysis2.4.2CCPNpeak 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: 10 / Conformers submitted total number: 10

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