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- PDB-9u6z: INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE AND RNAS WITH A ... -

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Basic information

Entry
Database: PDB / ID: 9u6z
TitleINTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE AND RNAS WITH A SINGLE BULGE
ComponentsDNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3')
KeywordsRNA / COMPLEX / FLUOROQUINOLONE
Function / homologyChem-53D / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / na
AuthorsIchijo, R. / Kawai, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biochem. / Year: 2025
Title: Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of the bulged residues.
Authors: Ichijo, R. / Kawai, G.
History
DepositionMar 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4582
Polymers6,0151
Non-polymers4441
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3')


Mass: 6014.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: Chemical ChemComp-53D / 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34FN5O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.36 mM DNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3'), 95% H2O/5% D2O0.36 mM RNA and 0.72 mM 53Dsample95% H2O/5% D2O
solution20.36 mM DNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3'), 95% H2O/5% D2Osample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.36 mMDNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3')none1
0.36 mMDNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3')none2
Sample conditionsDetails: 20 mM sodium phosphate buffer (pH 6.5) and 50 mM NaCl
Ionic strength: 50 mM / Label: condition / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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