BMRB Entry 30804

Name: Solution structure of the major MYC promoter G-quadruplex with a wild-type flanking in complex with NSC85697, a quinoline derivative
Published: 2021-06-18

Click here to enlarge.

PDB ID: 7kbw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30804
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:

Solution structure of the major MYC promoter G-quadruplex with a wild-type flanking in complex with NSC85697, a quinoline derivative

Deposition date:

2020-10-03

Original release date:

2021-06-18

Authors:

Dickerhoff, J.; Yang, D.

Citation:

Citation: Dickerhoff, Jonathan; Dai, Jixun; Yang, Danzhou. "Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes" Nucleic Acids Res. 49, 5905-5915 (2021).
PubMed: 33978746

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 7033.523 Da.
entity_WAM, non-polymer, 335.376 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: TGAGGGTGGGTAGGGTGGGG AA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	26
1H chemical shifts	218

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	2

Entities:

Entity 1, unit_1 22 residues - 7033.523 Da.

1

DT

DG

DA

DG

DT

DG

2

DT

DA

DG

DT

DG

3

DA

Entity 2, unit_2 - C20 H19 N2 O3 - 335.376 Da.

1

WAM

Samples:

sample_1: Myc2345 0.8 mM; NSC85697 2.4 mM; potassium phosphate 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 288 K

sample_conditions_3: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 308 K

Experiments:

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

Software:

Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 800 MHz