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- PDB-1i5v: SOLUTION STRUCTURE OF 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL IN... -

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Basic information

Entry
Database: PDB / ID: 1i5v
TitleSOLUTION STRUCTURE OF 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL INTERCALATED IN THE DNA DUPLEX D(CGATCG)2
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / DOUBLE HELIX
Function / homology2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsFavier, A. / Blackledge, M. / Simorre, J.P. / Marion, D. / Debousy, J.C.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of 2-(pyrido[1,2-e]purin-4-yl)amino-ethanol intercalated in the DNA duplex d(CGATCG)2.
Authors: Favier, A. / Blackledge, M. / Simorre, J.P. / Crouzy, S. / Dabouis, V. / Gueiffier, A. / Marion, D. / Debouzy, J.C.
History
DepositionMar 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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_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_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: 5'-D(*CP*GP*AP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0774
Polymers3,6182
Non-polymers4582
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 100The submitted conformer models are the 22 structures with the lowest experimental energy
RepresentativeModel #12closest to the average

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-PPZ / 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL


Mass: 229.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11N5O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
231DQF-COSY
241TOCSY
2511H-1H CT COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM 2-(pyrido[1,2-e]purin-4-yl)amino-ethanol, 2mM d(CGATCG)2 160 mM KCl, 0.15 mM EDTA, 20 mM sodium phosphate90% H2O/10% D2O
22 mM 2-(pyrido[1,2-e]purin-4-yl)amino-ethanol, 2mM d(CGATCG)2 160 mM KCl, 0.15 mM EDTA, 20 mM sodium phosphate100% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 7 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AMXBrukerAMX6002
Bruker AMXBrukerAMX4003

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Processing

NMR software
NameVersionClassification
VNMR6.Acollection
Felixprocessing
Insight97data analysis
Discoverstructure solution
Discoverrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: calculation from randomized cartesian coordinates
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 22 structures with the lowest experimental energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

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