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- PDB-1u6c: The NMR-derived solution structure of the (2S,3S)-N6-(2,3,4-trihy... -

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Entry
Database: PDB / ID: 1u6c
TitleThe NMR-derived solution structure of the (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide
Components((2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide) x 2
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
AuthorsScholdberg, T.A. / Nechev, L.N. / Merritt, W.K. / Harris, T.M. / Harris, C.M. / Lloyd, R.S. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 2004
Title: Structure of a site specific major groove (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide.
Authors: Scholdberg, T.A. / Nechev, L.V. / Merritt, W.K. / Harris, T.M. / Harris, C.M. / Lloyd, R.S. / Stone, M.P.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide
B: (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide


Theoretical massNumber of molelcules
Total (without water)6,8122
Polymers6,8122
Non-polymers00
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 / -
Representative

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Components

#1: DNA chain (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide


Mass: 3520.367 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 800 MHz

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Processing

RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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