BMRB Entry 30335

Name: NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence
Published: 2018-01-25

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PDB ID: 6asf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30335
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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 and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence

Deposition date:

2017-08-24

Original release date:

2018-01-25

Authors:

Harika, N.; Boykin, D.

Citation:

Citation: Harika, N.; Markus, M.; Wilson, W.. "First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences" Chemistry 23, 17612-17620 (2017).
PubMed: 29044822

Assembly members:

Assembly members:
DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'), polymer, 9 residues, 2748.838 Da.
DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'), polymer, 9 residues, 2721.796 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'): CCAAGATAG
DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'): CTATCTTGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	131

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

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

Entities:

Entity 1, entity_1 9 residues - 2748.838 Da.

1

DC

DA

DG

DA

DT

DA

DG

Entity 2, entity_2 9 residues - 2721.796 Da.

1

DC

DT

DA

DT

DC

DT

DG

Samples:

sample_1: DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3') 0.54 mM; DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3') 0.54 mM; DSS 0.4 mM; EDTA 0.14 mM; Tris-d11 buffer 10 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 0.5 mM; pH: 6.3 pH*; pressure: 1 atm; temperature: 285 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY 100MS	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 100MS	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 50MS	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 50MS	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 150MS	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 300MS	sample_1	isotropic	sample_conditions_1
2D 1H-1H CONSTANT TIME NOESY	sample_1	isotropic	sample_conditions_1
1D 31P	sample_1	isotropic	sample_conditions_1
1H, 31P-correlated 2D spectra (HPCOR)	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

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

SPARKY, Goddard,T.D.; Kneller,D.G. - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker AvanceIII 850 MHz