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- PDB-6sx3: Intercalation of heterocyclic ligand between quartets in G-rich t... -

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Basic information

Entry
Database: PDB / ID: 6sx3
TitleIntercalation of heterocyclic ligand between quartets in G-rich tetrahelical structure
ComponentsVK2
KeywordsDNA / Intercalation AGCGA-quadruplex G-quadruplex Heterocyclic ligand
Function / homologyChem-LWQ / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKotar, A. / Kocman, V. / Plavec, J.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-1704 Slovenia
Slovenian Research AgencyP1-0242 Slovenia
CitationJournal: Chemistry / Year: 2020
Title: Intercalation of a Heterocyclic Ligand between Quartets in a G-Rich Tetrahelical Structure.
Authors: Kotar, A. / Kocman, V. / Plavec, J.
History
DepositionSep 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 15, 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: VK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3382
Polymers9,8881
Non-polymers4501
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5690 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain VK2


Mass: 9888.333 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in PLEKHG3 human gene
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-LWQ / ~{N}2,~{N}6-bis(1-methylquinolin-1-ium-3-yl)pyridine-2,6-dicarboxamide


Mass: 449.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H23N5O2
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
121isotropic22D 1H-1H NOESY
131isotropic12D 1H-13C HSQC aromatic
142isotropic12D 1H-15N HSQC
152isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.35 mM VK2, 100 mM LiCl, 90% H2O/10% D2Ounlabelled90% H2O/10% D2O
solution20.35 mM 10% Residue-specific labrelling VK2, 100 mM LiCl, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2OResidue-specific partially 15N, 13C-labelled (10% guanine residues) oligonucleotides
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMVK2natural abundance1
100 mMLiClnatural abundance1
0.35 mMVK210% Residue-specific labrelling2
100 mMLiClnatural abundance2
Sample conditionsDetails: pH value of the samples was set to 6 with the use of LiOH and HCl.
Ionic strength: 100 mM / Label: Conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent ASC Agilent Technologies Superconducting MagnetAgilentASC Agilent Technologies Superconducting Magnet6001
Agilent Oxford Superconducting MagnetAgilentOxford Superconducting Magnet8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
VNMRVarianchemical shift assignment
SparkyGoddarddata analysis
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing6
simulated annealing7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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