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- PDB-2kvy: NMR solution structure of the 4:1 complex between an uncharged di... -

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Basic information

Entry
Database: PDB / ID: 2kvy
TitleNMR solution structure of the 4:1 complex between an uncharged distamycin A analogue and [d(TGGGGT)]4
ComponentsDNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
KeywordsDNA / G-Quadruplex / Coulombic Interactions / NMR titration / Distamycin A / Structure calculations / Isothermal Titration Calorimetry (ITC)
Function / homologyChem-KVY / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsCosconati, S. / Marinelli, L. / Trotta, R. / Virno, A. / De Tito, S. / Romagnoli, R. / Pagano, B. / Limongelli, V. / Giancola, C. / Baraldi, P. ...Cosconati, S. / Marinelli, L. / Trotta, R. / Virno, A. / De Tito, S. / Romagnoli, R. / Pagano, B. / Limongelli, V. / Giancola, C. / Baraldi, P. / Mayol, L. / Novellino, E. / Randazzo, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle.
Authors: Cosconati, S. / Marinelli, L. / Trotta, R. / Virno, A. / De Tito, S. / Romagnoli, R. / Pagano, B. / Limongelli, V. / Giancola, C. / Baraldi, P.G. / Mayol, L. / Novellino, E. / Randazzo, A.
History
DepositionMar 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,3958
Polymers7,5214
Non-polymers1,8744
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 1880.251 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-KVY / 4-amino-1-methyl-N-{1-methyl-5-[(1-methyl-5-{[3-(methylamino)-3-oxopropyl]carbamoyl}-1H-pyrrol-3-yl)carbamoyl]-1H-pyrrol-3-yl}-1H-pyrrole-2-carboxamide


Mass: 468.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H28N8O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-1H TOCSY
2212D 1H-1H COSY
1322D 1H-1H NOESY
2412D 1H-1H NOESY
2512D 1H-31P COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
18 mM KVY-1, 2 mM DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')-2, 100 % D2O-3, 10 mM potassium phosphate-4, 70 mM potassium chloride-5, 90% H2O/10% D2O90% H2O/10% D2O
28 mM KVY-6, 2 mM DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')-7, 10 % D2O-8, 10 mM potassium phosphate-9, 70 mM potassium chloride-10, 90 % H2O-11, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
8 mMKVY-11
2 mMDNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')-21
100 %D2O-31
10 mMpotassium phosphate-41
70 mMpotassium chloride-51
8 mMKVY-62
2 mMDNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')-72
10 %D2O-82
10 mMpotassium phosphate-92
70 mMpotassium chloride-102
90 %H2O-112
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1807ambient 298 K
2807ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA7001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
FelixCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmpeak picking
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 16 / NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 16 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 16 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 0
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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