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- PDB-202d: SOLUTION STRUCTURE OF THE MENOGARIL-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 202d
TitleSOLUTION STRUCTURE OF THE MENOGARIL-DNA COMPLEX
ComponentsDNA (5'-D(*GP*AP*CP*AP*TP*GP*TP*C)-3')
KeywordsDNA / MENOGARIL
Function / homologyMENOGARIL / DNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsChen, H. / Patel, D.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 1995
Title: Solution Structure of the Menogaril-DNA Complex
Authors: Chen, H. / Patel, D.J.
#1: Journal: Biochemistry / Year: 1989
Title: Antitumor Drug Nogalamycin Binds DNA in Both Grooves Simultaneously: Molecular Structure of Nogalamycin-DNA Complex
Authors: Liaw, Y.-C. / Gao, Y.-G. / Robinson, H. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.
History
DepositionMar 29, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*CP*AP*TP*GP*TP*C)-3')
B: DNA (5'-D(*GP*AP*CP*AP*TP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9364
Polymers4,8532
Non-polymers1,0832
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4all calculated structures submitted
Representative

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: Chemical ChemComp-MNG / MENOGARIL


Mass: 541.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31NO10 / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: MENOGARIL WAS PROVIDED BY UPJOHN CO., KALAMAZOO, MICHIGAN.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A ...Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 100, 150 AND 200 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.039 0.038 0.038 0.036 BOND (ANG) 0.012 0.012 0.012 0.011 ANGLES (DEG) 3.833 3.818 3.776 3.684 IMPROPERS (DEG) 0.251 0.250 0.286 0.219
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 4 / Conformers submitted total number: 4

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