BMRB Entry 34611

Name: Three-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate
Published: 2021-08-02

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PDB ID: 7nwd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34611
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Three-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate PubMed: 34365512

Deposition date: 2021-03-16 Original release date: 2021-08-02

Authors: Peterkova, K.; Durnik, I.; Marek, R.; Plavec, J.; Podbevsek, P.

Citation: Peterkova, K.; Durnik, I.; Marek, R.; Plavec, J.; Podbevsek, P.. "c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry" Nucleic Acids Res. 49, 8947-8960 (2021).

Assembly members:
entity_1, polymer, 21 residues, 6771.506 Da.
entity_K, non-polymer, 39.098 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: XGGGCGGGCGCTAGGGAGGG T

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	32
1H chemical shifts	134

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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 21 residues - 6771.506 Da.

1

UTB

DG

DC

DG

DC

DG

2

DC

DT

DA

DG

DA

DG

3

DT

Entity 2, unit_2 - K - 39.098 Da.

1

K

Samples:

sample_1: c-kit2_py1 1.0 ± 0.1 mM; potassium phosphate 5 ± 0.5 mM; potassion chloride 20 ± 1.0 mM

sample_conditions_1: ionic strength: 25 mM; pH: 7.0; 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-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v4.0.7, Bruker Biospin - collection

NMRFAM-SPARKY, National Magnetic Resonance Facility at Madison - chemical shift assignment

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

NMR spectrometers:

Bruker Bruker AVANCE NEO 600 MHz NMR spectrometer 600 MHz