BMRB Entry 34960

Name: Quadruplex-duplex hybrids (QDH) complex with PhenDC3 from PIM1 oncogene.
Published: 2025-08-29

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PDB ID: 9gvi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34960
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Quadruplex-duplex hybrids (QDH) complex with PhenDC3 from PIM1 oncogene.

Deposition date:

2024-09-24

Original release date:

2025-08-29

Authors:

Ghosh, A.; Lenarcic, M.; Trantirek, L.; Harnos, J.

Citation:

Citation: Ghosh, A.; Lenarcic, M.; Trantirek, L.; Harnos, J.. "Quadruplex-duplex hybrids (QDH) complex with PhenDC3 from PIM1 oncogene." .

Assembly members:

Assembly members:
entity_1, polymer, 27 residues, 8506.419 Da.
entity_PQ3, non-polymer, 550.609 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: GCGGGAGGGCGCGCCAGCGG GGTCGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	189

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

Entities:

Entity 1, unit_1 27 residues - 8506.419 Da.

1

DG

DC

DG

DA

DG

DC

2

DG

DC

DG

DC

DA

DG

DC

DG

3

DG

DT

DC

DG

Entity 2, unit_2 - C34 H26 N6 O2 - 550.609 Da.

1

PQ3

Samples:

sample_1: SO7-PhenDC3 500 uM; SO7-PhenDC3, [U-13C; U-15N]-Guanine, 200 uM; KCl 20 mM; potassium phosphate 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 7.1; pressure: 1 atm; temperature: 298.2 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 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

Software:

NMRFAM-SPARKY v1.414, Woonghee Lee, Marco Tonelli, and John L. Markley - chemical shift assignment, peak picking

Amber v22, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE NEO 950 MHz
Bruker AVANCE NEO 850 MHz
Bruker AVANCE NEO 600 MHz