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- PDB-6kxz: HUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 EPIRU... -

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Basic information

Entry
Database: PDB / ID: 6kxz
TitleHUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 EPIRUBICIN (EPI) MOLECULES
Components[TTAGGGT]4-EPI-Complex
KeywordsDNA / G-QUADRUPLEX / EPIRUBICIN / EPIADRIAMYCIN
Function / homology4'-EPIDOXORUBICIN / DNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsCHAIN A, B, C, D, L
AuthorsBarthwal, R. / Raje, S. / Pandav, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)] 4 by anticancer drug epirubicin.
Authors: Barthwal, R. / Raje, S. / Pandav, K.
History
DepositionSep 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 3, 2021Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.type
Revision 2.1Sep 29, 2021Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 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

Downloads & links

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Assembly

Deposited unit
A: [TTAGGGT]4-EPI-Complex
B: [TTAGGGT]4-EPI-Complex
C: [TTAGGGT]4-EPI-Complex
D: [TTAGGGT]4-EPI-Complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7636
Polymers8,6744
Non-polymers1,0892
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3590 Å2
ΔGint-21 kcal/mol
Surface area5470 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 35structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: DNA chain
[TTAGGGT]4-EPI-Complex


Mass: 2168.445 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DT5 = THY at 5' Ter DT3 = THY at 3' Ter / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-DM6 / 4'-EPIDOXORUBICIN / 4'-EPIADRIAMYCIN / Epirubicin


Mass: 544.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H30NO11 / Comment: medication, chemotherapy*YM
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
111isotropic11D
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1.11 mM (DT5)TAGGG(DT3), 2.22 mM Epirubicin, 90% H2O/10% D2O
Label: 1H / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.11 mM(DT5)TAGGG(DT3)natural abundance1
2.22 mMEpirubicinnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: Condition_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AmberCASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMANrefinement
TopSpin3.6structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 15

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