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- PDB-7x3a: NMR solution structure of the 1:1 complex of a pyridostatin (PDS)... -

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Basic information

Entry
Database: PDB / ID: 7x3a
TitleNMR solution structure of the 1:1 complex of a pyridostatin (PDS) bound to a G-quadruplex MYT1L
ComponentsG-quadruplex DNA MYT1L
KeywordsDNA / G-quadruplex / Complex
Function / homologyChem-7V8 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, L.-Y. / Mao, Z.-W. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Structural Basis of Pyridostatin and Its Derivatives Specifically Binding to G-Quadruplexes.
Authors: Liu, L.-Y. / Ma, T.Z. / Zeng, Y.L. / Liu, W. / Mao, Z.-W.
History
DepositionFeb 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: 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
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 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: G-quadruplex DNA MYT1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8142
Polymers9,2171
Non-polymers5971
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
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 G-quadruplex DNA MYT1L


Mass: 9216.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-7V8 / 4-(2-azanylethoxy)-N2,N6-bis[4-(2-azanylethoxy)quinolin-2-yl]pyridine-2,6-dicarboxamide / Pyridostatin


Mass: 596.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H32N8O5 / 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 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H COSY
241isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM / MYT1L, 1.0 mM / PDS, 90% H2O/10% D2OPDS-MYT1L90% H2O/10% D2O
solution21.2 mM / MYT1L, 90% H2O/10% D2OMYT1L90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMYT1L/1
1.0 mMPDS/1
1.2 mMMYT1L/2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
140 mM25C71 atm298 K
240 mM5C71 atm278 K

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NMR measurement

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

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.27data extraction
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 4.26 Å2 / Biso mean: 0.7116 Å2 / Biso min: 0.19 Å2
NMR software
NameDeveloperClassification
X-PLORBrungerrefinement
X-PLORBrungerstructure calculation
NMRFAM-SPARKYWoonghee Leechemical shift assignment
NMRFAM-SPARKYWoonghee Leepeak 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: 100 / Conformers submitted total number: 15

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