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- PDB-1pqq: NMR Structure of a Cyclic Polyamide-DNA Complex -

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Entry
Database: PDB / ID: 1pqq
TitleNMR Structure of a Cyclic Polyamide-DNA Complex
Components
  • 5'-D(*CP*GP*CP*TP*AP*AP*CP*AP*GP*GP*C)-3'
  • 5'-D(*GP*CP*CP*TP*GP*TP*TP*AP*GP*CP*G)-3'
KeywordsDNA
Function / homologyChem-CYE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsZhang, Q. / Dwyer, T.J. / Tsui, V. / Case, D.A. / Cho, J. / Dervan, P.B. / Wemmer, D.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: NMR Structure of a Cyclic Polyamide-DNA Complex.
Authors: Zhang, Q. / Dwyer, T.J. / Tsui, V. / Case, D.A. / Cho, J. / Dervan, P.B. / Wemmer, D.E.
History
DepositionJun 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,6563
Polymers6,7082
Non-polymers9481
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 20
RepresentativeModel #21average structure

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Components

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


Mass: 3343.200 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*CP*TP*GP*TP*TP*AP*GP*CP*G)-3'


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CYE / 45-(3-AMINOPROPYL)-5,11,22,28,34-PENTAMETHYL-3,9,15,20,26,32,38,43-OCTAOXO-2,5,8,14,19,22,25,28,31,34,37,42,45,48-TETRADECAAZA-11-AZONIAHEPTACYCLO[42.2.1.1~4,7~.1~10,13~.1~21,24~.1~27,30~.1~33,36~]DOPENTACONTA-1(46),4(52),6,10(51),12,21(50),23,27(49),29,33(48),35,44(47)-DODECAENE


Mass: 948.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H55N16O8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

NMR representativeSelection criteria: average structure
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 21

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