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- PDB-1ddp: Solution structure of a CISPLATIN-INDUCED [CATAGCTATG]2 Interstra... -

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Basic information

Entry
Database: PDB / ID: 1ddp
TitleSolution structure of a CISPLATIN-INDUCED [CATAGCTATG]2 Interstrand cross-link
ComponentsDNA (5'-D(*CP*AP*TP*AP*GP*CP*TP*AP*TP*G)-3')
KeywordsDNA / DOUBLE HELIX / ANTITUMOR DRUG / CIS-DDP / INTERSTRAND CROSS-LINK
Function / homologyCisplatin / DNA
Function and homology information
MethodSOLUTION NMR
AuthorsZhu, L. / Huang, H. / Reid, B.R. / Drobny, G.P. / Hopkins, P.B.
CitationJournal: Science / Year: 1995
Title: Solution structure of a cisplatin-induced DNA interstrand cross-link.
Authors: Huang, H. / Zhu, L. / Reid, B.R. / Drobny, G.P. / Hopkins, P.B.
History
DepositionOct 26, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,3883
Polymers6,0882
Non-polymers3001
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -
Representative

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Components

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


Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Details: CHEMICALLY SYNTHESIZED / Comment: medication, chemotherapy*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: BECAUSE THE BOND LENGTH BETWEEN PT AND N7 IN THE CISPLATIN CROSS-LINK IS LONGER THAN 2.00 ANGSTROMS, THE PT-N7 BONDS MIGHT NOT APPEAR WHEN A PROGRAM READS THIS ENTRY.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR softwareName: Discover / Developer: BIOSYM TECHNOLOGIES / Classification: refinement
RefinementSoftware ordinal: 1
Details: FINAL RMS COORD. SHIFT 0.55 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 643 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 AMBER FORCE FIELDS USED
NMR ensembleConformers submitted total number: 10

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