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- PDB-1n37: NMR Solution Structure of the Anthracycline Respinomycin D Interc... -

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Entry
Database: PDB / ID: 1n37
TitleNMR Solution Structure of the Anthracycline Respinomycin D Intercalation Complex with a Double Stranded DNA Molecule (AGACGTCT)2
Components5'-D(*AP*GP*AP*CP*GP*TP*CP*T)-3'
KeywordsDNA / drug-DNA recognition / anthracycline antibiotcs / Respinomycin D / molecular dynamics simulations / NMR spectroscopy
Function / homologyRESPINOMYCIN D / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsMaynard, A.J. / Williams, H.E.L. / Searle, M.S.
CitationJournal: Org.Biomol.Chem. / Year: 2003
Title: DNA recognition by the Anthracycline Antibiotic Respinomycin D: NMR Structure of the Intercalation Complex with d(AGACGTCT)2
Authors: Searle, M.S. / Maynard, A.J. / Williams, H.E.L.
History
DepositionOct 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,9213
Polymers4,8532
Non-polymers1,0681
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-RSD / RESPINOMYCIN D


Mass: 1068.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H75N2O22

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: Respinomycin D, D(AGACGTCT)2, TSP, NaN3, Na-ETDA / Solvent system: D2O
Sample conditionsIonic strength: 100mM NaCl 10mM Na2HPO4 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SANDER(AMBER)4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANstructure solution
SANDER(AMBER)4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Sample was subjected to 500ps of restrained molecular dynamics. Using the AMBER94 Force Field
NMR ensembleConformers submitted total number: 1

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