BMRB Entry 36682
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36682
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry
Citation: Ichijo, Rika; Kawai, Gota. "Specific Interaction between a Fluoroquinolone Derivative, KG022, and RNAs with a Single Bulge." Biochemistry 64, 2192-2199 (2025).
PubMed: 40067027
Assembly members:
RNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3'), polymer, 19 residues, 6015.592 Da.
1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide, non-polymer, 443.557 Da.
Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus
Experimental source: Production method: chemical synthesis Host organism: unidentified
Entity Sequences (FASTA):
RNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3'): GGAUACUUUCGAGUCAUCC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 72 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_53D | 2 |
Entities:
Entity 1, entity_1 19 residues - 6015.592 Da.
| 1 | G | G | A | U | A | C | U | U | U | C | ||||
| 2 | G | A | G | U | C | A | U | C | C |
Entity 2, entity_53D - C24 H34 F N5 O2 - 443.557 Da.
| 1 | 53D |
Samples:
sample_1: RNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3') 0.44 mM; 53D 0.66 mM; NaCl 50 mM; Na2HPO4/NaH2PO4 20 mM; H2O 95%; D2O, [U-2H], 5%
sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
Sparky v3, Goddard - chemical shift assignment
CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation
Sparky v3, Goddard - peak picking
NMR spectrometers:
- Bruker AVANCE NEO 600 MHz