BMRB Entry 35018

Name: NMR structure of AT-rich DNA bound to the minor groove ligand JNII40
Published: 2025-10-17

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PDB ID: 9sqc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR35018
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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:

NMR structure of AT-rich DNA bound to the minor groove ligand JNII40

Deposition date:

2025-09-22

Original release date:

2025-10-17

Authors:

Garavis, M.; Ugedo, C.

Citation:

Citation: Nue, J.; Ugedo, C.; Lagartera, L.; Gonzalez, C.; Dardonville, C.; Garavis, M.. "Solution structure of an antileishmanial drug bound to AT-DNA" .

Assembly members:

Assembly members:
entity_1, polymer, 10 residues, 3043.029 Da.
entity_2, non-polymer, 435.481 Da.
entity_HOH, water, 18.015 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: recombinant technology Host organism: synthetic construct

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CATATATATG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	124

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	1
3	unit_3	2
4	unit_4	3
5	unit_5	3

Entities:

Entity 1, unit_1 10 residues - 3043.029 Da.

1

DC

DA

DT

DA

DT

DA

DT

DA

DT

DG

Entity 2, unit_3 - 435.481 Da.

1

A1JPP

Entity 3, unit_4 - 18.015 Da.

1

HOH

Samples:

sample_1: DNA (5'-D(*CP*AP*TP*AP*TP*AP*TP*AP*TP*G)-3') 400 uM; JNII40 400 uM; sodium phosphate 10 mM; sodium chloride 100 mM

sample_2: DNA (5'-D(*CP*AP*TP*AP*TP*AP*TP*AP*TP*G)-3') 300 uM; JNII40 300 uM; sodium phosphate 10 mM; sodium chloride 100 mM

sample_conditions_1: ionic strength: 110 mM; pH: 6.3; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - refinement

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

Poky, Manthey, Tonelli, Clos II, Rahimi, Markley and Lee - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE NEO 600 MHz