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- PDB-1kvh: NCSi-gb-bulge-DNA complex induced formation of a DNA bulge struct... -

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Basic information

Entry
Database: PDB / ID: 1kvh
TitleNCSi-gb-bulge-DNA complex induced formation of a DNA bulge structure by a molecular wedge ligand-post-activated neocarzinostatin chromophore
Components
  • 5'-D(*CP*CP*CP*GP*AP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*AP*TP*TP*CP*GP*GP*G)-3'
KeywordsDNA
Function / homologyChem-NCS / DNA
Function and homology information
MethodSOLUTION NMR / distance geometry (DG), restrained molecular dynamics (rMDS), and relaxation matrix refinement
AuthorsGao, X. / Stassinopoulos, A. / Ji, J. / Kwon, Y. / Bare, S. / Goldberg, I.H.
CitationJournal: Biochemistry / Year: 2002
Title: Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore.
Authors: Gao, X. / Stassinopoulos, A. / Ji, J. / Kwon, Y. / Bare, S. / Goldberg, I.H.
History
DepositionJan 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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 / _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(*CP*CP*CP*GP*AP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*AP*TP*TP*CP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1353
Polymers5,4732
Non-polymers6631
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 7all calculated structures submitted
Representative

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Components

#1: DNA chain 5'-D(*CP*CP*CP*GP*AP*TP*GP*C)-3'


Mass: 2387.581 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*AP*AP*TP*TP*CP*GP*GP*G)-3'


Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-NCS / SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]]


Mass: 662.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H36NO12

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
242PE-COSY
252TOCSY, H-P COSY
NMR detailsText: This structure was determined using 2D homonuclear and heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
1ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 90% H2O, 10% D2O90% H2O/10% D2O
2ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O99.96% D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
10.1M NACL, 10 mM SODIUM PHOSPHATE 6.4 270 K
20.1M NACL, 10 mM SODIUM PHOSPHATE 6.4 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.01 / Developer: Brunger / Classification: refinement
RefinementMethod: distance geometry (DG), restrained molecular dynamics (rMDS), and relaxation matrix refinement
Software ordinal: 1
Details: A total of 681 NMR restraints is used to derive the final refined structures. The total restraints consist of 590 of NOE-derived distance restraints and 91 of dihedral angle restraints. ...Details: A total of 681 NMR restraints is used to derive the final refined structures. The total restraints consist of 590 of NOE-derived distance restraints and 91 of dihedral angle restraints. Especially, 85 of intermolecular distance restraints are derived which represent the interaction between the drug and the bulge duplex.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 7 / Conformers submitted total number: 7

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