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- PDB-6lnz: NMR solution structure of VEGF G-quadruplex bound a non-planar cy... -

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Basic information

Entry
Database: PDB / ID: 6lnz
TitleNMR solution structure of VEGF G-quadruplex bound a non-planar cyclometalated-carbene platinum(II) complex
ComponentsDNA (5'-D(*CP*GP*GP*GP*GP*CP*GP*GP*GP*CP*CP*TP*TP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')
KeywordsDNA / VEGF G-quadruplex / solution structure / DNA-ligand complex / platinum complex
Function / homologycyclometalated-carbene platinum(II) complex / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsLiu, W. / Zhu, B.Z. / Mao, Z.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21837006 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Selectivity and Targeting of G-Quadruplex Binders Activated by Adaptive Binding and Controlled by Chemical Kinetics.
Authors: Zhu, B.C. / He, J. / Liu, W. / Xia, X.Y. / Liu, L.Y. / Liang, B.B. / Yao, H.G. / Liu, B. / Ji, L.N. / Mao, Z.W.
History
DepositionJan 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: 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(*CP*GP*GP*GP*GP*CP*GP*GP*GP*CP*CP*TP*TP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4672
Polymers6,9221
Non-polymers5441
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*CP*GP*GP*GP*GP*CP*GP*GP*GP*CP*CP*TP*TP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3') / VEGF G-quadruplex DNA


Mass: 6922.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-EL9 / cyclometalated-carbene platinum(II) complex


Mass: 544.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15F2N4Pt / 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
111isotropic22D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
131isotropic22D 1H-1H TOCSY
241isotropic12D 1H-1H TOCSY
151isotropic22D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM VEGF G-quadruplex DNA, 1.0 mM LLPtCl, 75 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O
Label: Sample-1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMVEGF G-quadruplex DNAnatural abundance1
1.0 mMLLPtClnatural abundance1
75 mMpotassium chloridenatural abundance1
25 mMpotassium phosphatenatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM25C7.0 1 atm298 K
2100 mM5C7.0 1 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Discovery StudioBIOVIAstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing1
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: 15

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