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- PDB-107d: SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX -

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Basic information

Entry
Database: PDB / ID: 107d
TitleSOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX
Components
  • DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3')
KeywordsDNA / DOUBLE HELIX
Function / homologyChem-DUO / DNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsLin, C.H. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution structure of the covalent duocarmycin A-DNA duplex complex.
Authors: Lin, C.H. / Patel, D.J.
History
DepositionJan 17, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,7443
Polymers4,2352
Non-polymers5101
Water0
1


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

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Components

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


Mass: 2039.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3')


Mass: 2195.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#3: Chemical ChemComp-DUO / 4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER / DUOCARMYCIN A


Mass: 509.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N3O8 / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., JAPAN.

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
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 2-D NMR DATA. ONE INITIAL VELOCITY SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR STRUCTURES. 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 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310-0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS.
NMR ensembleConformers submitted total number: 4

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