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- PDB-1x95: Solution structure of the DNA-hexamer ATGCAT complexed with DNA B... -

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Basic information

Entry
Database: PDB / ID: 1x95
TitleSolution structure of the DNA-hexamer ATGCAT complexed with DNA Bis-intercalating Anticancer Drug XR5944 (MLN944)
Components5'-D(*AP*TP*GP*CP*AP*T)-3'
KeywordsDNA / anticancer drug / transcription inhibition / novel DNA binding / AP-1 / MLN944
Function / homologyChem-XR2 / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsDai, J. / Punchihewa, C. / Mistry, P. / Ooi, A.T. / Yang, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Novel DNA bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug.
Authors: Dai, J. / Punchihewa, C. / Mistry, P. / Ooi, A.T. / Yang, D.
History
DepositionAug 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Other / Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*AP*TP*GP*CP*AP*T)-3'
B: 5'-D(*AP*TP*GP*CP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2073
Polymers3,6162
Non-polymers5911
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain 5'-D(*AP*TP*GP*CP*AP*T)-3'


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized using solid phase DNA synthesizer
#2: Chemical ChemComp-XR2 / 1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM


Mass: 590.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38N8O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D NOESY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1-4mM DNA oligonucleotides; MLN944/DNA 1:1 ; 50mM sodium phosphate buffer at pH 7; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate buffer / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
Sparky3.1Goddard T.D. ; Kneller, D. G.data analysis
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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