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- PDB-1cx3: SOLUTION STRUCTURE OF A COMPLEX BETWEEN D(ATGCAT)2 AND THE ANTITU... -

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Basic information

Entry
Database: PDB / ID: 1cx3
TitleSOLUTION STRUCTURE OF A COMPLEX BETWEEN D(ATGCAT)2 AND THE ANTITUMOR BISNAPHTHALIMIDE LU-79553
ComponentsDNA (5'-D(*AP*TP*GP*CP*AP*T)-3')
KeywordsDNA / TOPOISOMERASE / ANTICANCER / NAPHTHALIMIDE / INTERCALATION / DEOXYRIBONUCLEIC ACID
Function / homologyN,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE / DNA
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS
AuthorsGallego, J. / Reid, B.R.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure and dynamics of a complex between DNA and the antitumor bisnaphthalimide LU-79553: intercalated ring flipping on the millisecond time scale.
Authors: Gallego, J. / Reid, B.R.
History
DepositionAug 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,1393
Polymers3,6162
Non-polymers5231
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 / 20STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Representative

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Components

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


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA DOUBLE HELIX INTERCALATED BY LU-79553
#2: Chemical ChemComp-NF / N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE / LU-79553


Mass: 522.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H30N4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121NOESY
131ROESY
141TOCSY
151HP-HETCOR

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Sample preparation

DetailsContents: SODIUM PHOSPHATE, EDTA
Sample conditionsIonic strength: 20 mM SODIUM PHOSPHATE / pH: 7.20 / Pressure: 1 atm / Temperature: 275.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
BIRDER1995ZHU AND REIDrefinement
DGIIstructure solution
Amberstructure solution
BIRDERstructure solution
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 15

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