BMRB Entry 30688

Name: Molecular Recognition of Guanine Metabolites and Drugs by Vacancy-Bearing G-Quadruplex in the PDGFR-b Promoter
Published: 2020-03-05

Click here to enlarge.

PDB ID: 6v0l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30688
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

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:

Citation: Wang, Kai-Bo; Dickerhoff, Jonathan; Wu, Guanhui; Yang, Danzhou. "PDGFR-beta Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs" J. Am. Chem. Soc. 142, 5204-5211 (2020).
PubMed: 32101424

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XAGGGAGGGCGGCGGGACA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	178

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 19 residues - 5929.906 Da.

1

3D1

DA

DG

DA

DG

DC

2

DG

DC

DG

DA

DC

DA

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_1	isotropic	sample_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