BMRB Entry 19592
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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/BMR19592
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Title: Molecular Binding of TFF1 Estrogen Response Element by a DNA Bis-intercalating Anticancer Drug XR5944 PubMed: 24711371
Deposition date: 2013-10-30 Original release date: 2014-04-11
Authors: Lin, Clement
Citation: Lin, Clement; Mathad, Raveendra; Zhang, Zhenjiang; Sidell, Neil; Yang, Danzhou. "Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator." Nucleic Acids Res. 42, 6012-6024 (2014).
Assembly members:
DNA_Strand_1, polymer, 15 residues, Formula weight is not available
DNA_Strand_2, polymer, 15 residues, Formula weight is not available
1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM, non-polymer, 590.718 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_Strand_1: AGGTCACGGTGGCCA
DNA_Strand_2: TGGCCACCGTGACCT
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 287 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | 5'-D(*AP*GP*GP*TP*CP*AP*CP*GP*GP*TP*GP*GP*CP*CP*A)-3' | 1 |
| 2 | 5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3' | 2 |
| 3 | XR5944, 1 | 3 |
| 4 | XR5944, 2 | 3 |
Entities:
Entity 1, 5'-D(*AP*GP*GP*TP*CP*AP*CP*GP*GP*TP*GP*GP*CP*CP*A)-3' 15 residues - Formula weight is not available
| 1 | DA | DG | DG | DT | DC | DA | DC | DG | DG | DT | ||||
| 2 | DG | DG | DC | DC | DA |
Entity 2, 5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3' 15 residues - Formula weight is not available
| 1 | DT | DG | DG | DC | DC | DA | DC | DC | DG | DT | ||||
| 2 | DG | DA | DC | DC | DT |
Entity 3, XR5944, 1 - C34 H38 N8 O2 - 590.718 Da.
| 1 | XR2 |
Samples:
sample_1: DNA (5, -D(*(X)*(X))-3')', 300; 2, sodium phosphate, ; 3, D2O, ;
sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
XWINNMR, Bruker Biospin - collection
SPARKY, Goddard - chemical shift assignment
X-PLOR, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Bruker Avance 600 MHz