BMRB Entry 17422
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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/BMR17422
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Title: Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir PubMed: 21280608
Deposition date: 2011-01-22 Original release date: 2011-02-09
Authors: Julien, Olivier; Beadle, James; Magee, Wendy; Chatterjee, Subhrangsu; Hostetler, Karl; Evans, David; Sykes, Brian
Citation: Julien, Olivier; Beadle, James; Magee, Wendy; Chatterjee, Subhrangsu; Hostetler, Karl; Evans, David; Sykes, Brian. "Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir." J. Am. Chem. Soc. 133, 2264-2274 (2011).
Assembly members:
Cidofovir_DNA_duplex_chain_A, polymer, 12 residues, Formula weight is not available
Cidofovir_DNA_duplex_chain_B, polymer, 12 residues, Formula weight is not available
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):
Cidofovir_DNA_duplex_chain_A: CGCATGXTACGC
Cidofovir_DNA_duplex_chain_B: GCGTAGCATGCG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 4 |
| 1H chemical shifts | 162 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Cidofovir DNA duplex, chain A | 1 |
| 2 | Cidofovir DNA duplex, chain B | 2 |
Entities:
Entity 1, Cidofovir DNA duplex, chain A 12 residues - Formula weight is not available
| 1 | DC | DG | DC | DA | DT | DG | L8P | DT | DA | DC | ||||
| 2 | DG | DC |
Entity 2, Cidofovir DNA duplex, chain B 12 residues - Formula weight is not available
| 1 | DG | DC | DG | DT | DA | DG | DC | DA | DT | DG | ||||
| 2 | DC | DG |
Samples:
sample_1: Cidofovir DNA duplex, chain_A 2 mM; Cidofovir DNA duplex, chain_B 2 mM; NaCl 50 mM; Na2HPO4 20 mM; EDTA 1 mM; DSS-d6 0.25 mM
sample_conditions_1: ionic strength: 70 mM; pH: 7.1; pressure: 1 atm; temperature: 298 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 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
VNMRJ v2.1B, Varian - collection
NMRPipe v4.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView v8.0.b30, Johnson, One Moon Scientific - chemical shift assignment
MARDIGRAS, T.L. James - NOE calibration
AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution
CORMA, T.L. James - structure validation
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian INOVA 500 MHz