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- PDB-1dsi: Solution structure of a duocarmycin sa-indole-alkylated dna dupleX -

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Basic information

Entry
Database: PDB / ID: 1dsi
TitleSolution structure of a duocarmycin sa-indole-alkylated dna dupleX
Components
  • DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DUOCARMYCIN / MINOR GROOVE BINDING / ANTITUMOR AGENT / LIGAND-DNA COMPLEX
Function / homologyChem-DSI / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NAB TO GENERATE A FAMILY OF CONFOMRERS THAT SAMPLE A WIDE RANGE OF CONFORMATIONAL SPACE. RESTRAINED MOLECULAR DYNAMICS TO GENERATE A RANGE OF STARTING STRUCTURES FOR DSI. PAIRS OF DNA, DSI STRUCTURES WERE THEN DOCKED, ITERATIVELY REFINED BY A SERIES OF RESTRAINED MOLECULAR DYNAMICS CALCULATIONS.
AuthorsSchnell, J.R. / Ketchem, R.R. / Boger, D.L. / Chazin, W.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 1999
Title: Binding-Induced Activation of DNA Alkylation by Duocarmycin SA: Insights from the Structure of an Indole Derivative-DNA Adduct
Authors: Schnell, J.R. / Ketchem, R.R. / Boger, D.L. / Chazin, W.J.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: High Resolution Solution Structure of a DNA Duplex Alkylated by the Antitumor Agent Duocarmycin Sa
Authors: Eis, P.S. / Smith, J.A. / Rydzewski, J.M. / Case, D.A. / Boger, D.L. / Chazin, W.J.
#2: Journal: J.Am.Chem.Soc. / Year: 1997
Title: Duocarmycin Sa Shortened, Simplified, and Extended Agents: A Systematic Examination of the Role of the DNA Binding Subunit
Authors: Boger, D.L. / Herzog, D.L. / Bollinger, B. / Johnson, D.S. / Cai, H. / Goldberg, J. / Turnbull, P.
History
DepositionJul 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3')
B: DNA (5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0953
Polymers6,7052
Non-polymers3891
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LOWEST RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

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


Mass: 3357.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MINOR GROOVE BOUND DUOCARMYCIN SA-INDOLE
#2: DNA chain DNA (5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3')


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MINOR GROOVE BOUND DUOCARMYCIN SA-INDOLE
#3: Chemical ChemComp-DSI / 4-HYDROXY-6-(1H-INDOLE-2-CARBONYL)-8-METHYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER / (+)DUOCARMYCIN SA-INDOLE


Mass: 389.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N3O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
1412Q
151P.E. COSY
1611H-13C HSQC
1711D 31P
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H NMR DATA. RESONANCE ASSIGNMENTS WERE AIDED BY A 1H - 13C HSQC EXPERIMENT PERFORMED AT NATURAL ISOTOPE ABUNDANCE.

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Sample preparation

Sample conditionsIonic strength: 150mM / pH: 7.0 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber5.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
Felix97structure solution
NAB2.1structure solution
MARDIGRAS5.21structure solution
Amber5.1structure solution
RefinementMethod: NAB TO GENERATE A FAMILY OF CONFOMRERS THAT SAMPLE A WIDE RANGE OF CONFORMATIONAL SPACE. RESTRAINED MOLECULAR DYNAMICS TO GENERATE A RANGE OF STARTING STRUCTURES FOR DSI. PAIRS OF DNA, DSI ...Method: NAB TO GENERATE A FAMILY OF CONFOMRERS THAT SAMPLE A WIDE RANGE OF CONFORMATIONAL SPACE. RESTRAINED MOLECULAR DYNAMICS TO GENERATE A RANGE OF STARTING STRUCTURES FOR DSI. PAIRS OF DNA, DSI STRUCTURES WERE THEN DOCKED, ITERATIVELY REFINED BY A SERIES OF RESTRAINED MOLECULAR DYNAMICS CALCULATIONS.
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST RESTRAINT VIOLATIONS / Conformers calculated total number: 40 / Conformers submitted total number: 20

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