BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 30688

Title: Molecular Recognition of Guanine Metabolites and Drugs by Vacancy-Bearing G-Quadruplex in the PDGFR-b Promoter

Deposition date: 2019-11-18 Original release date: 2020-03-05

Authors: Wang, K.; Dickerhoff, J.; Wu, G.; Yang, D.

Citation: Wang, K.; Wu, G.; Dickerhoff, J.; Yang, D.. "Molecular Recognition of Guanine Metabolites and Drugs by Vacancy-Bearing G-Quadruplex in the PDGFR-b Promoter"  . ., .-..

Assembly members:
entity_1, polymer, 19 residues, 5929.906 Da.
entity_DGP, non-polymer, 347.221 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: XAGGGAGGGCGGCGGGACA

Data sets:
Data typeCount
1H chemical shifts178

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 19 residues - 5929.906 Da.

1   3D1DADGDGDGDADGDGDGDC
2   DGDGDCDGDGDGDADCDA

Entity 2, entity_2 - C10 H14 N5 O7 P - 347.221 Da.

1   DGP

Samples:

sample_1: entity_1 3600 uM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 760 mmHg; temperature: 288 K

sample_conditions_2: ionic strength: 50 mM; pH: 7; pressure: 760 mmHg; temperature: 298 K

sample_conditions_3: ionic strength: 50 mM; pH: 7; pressure: 760 mmHg; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_3
2D 1H-13C HSQCsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_2

Software:

Sparky, Goddard - chemical shift assignment, peak picking

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

TopSpin, Bruker Biospin - processing

NMR spectrometers:

  • Bruker AVANCE III 800 MHz