BMRB Entry 17788

Name: Minor conformer of the DNA-peptide conjugate bridged by trimethylene tether
Published: 2014-04-23

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17788

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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:

Minor conformer of the DNA-peptide conjugate bridged by trimethylene tether

Deposition date:

2011-07-18

Original release date:

2014-04-23

Authors:

Huang, Hai; Kozekov, Ivan; Rizzo, Carmelo; McCullough, Amanda; LLoyd, R.; Stone, Michael

Citation:

Citation: Huang, Hai; Wang, Hao; Voehler, Markus; Kozekova, Albena; Rizzo, Carmelo; McCullough, Amanda; Lloyd, R. Stephen; Stone, Michael. "-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage." Chem. Res. Toxicol. 24, 1123-1133 (2011).
PubMed: 21561113

Assembly members:

Assembly members:
DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_, polymer, 12 residues, 3045.029 Da.
DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_, polymer, 12 residues, 3045.029 Da.
entity_3, polymer, 5 residues, 591.773 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available 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(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_: GCTAGCGAGTCC
DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_: GGACTCGCTAGC
entity_3: XKWKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	177

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_(5'-D(PCPTPAPGPCPGPAPGPTPC)-3')	1
2	DNA_(5'-D(PGPAPCPTPCPGPCPTPAPG)-3')	2
3	entity_3	3

Entities:

Entity 1, DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 12 residues - 3045.029 Da.

1

DG

DC

DT

DA

DG

DC

DG

DA

DG

DT

2

DC

Entity 2, DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 12 residues - 3045.029 Da.

1

DG

DA

DC

DT

DC

DG

DC

DT

DA

2

DG

DC

Entity 3, entity_3 5 residues - 591.773 Da.

1

TME

LYS

TRP

LYS

Samples:

sample_1: DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 1 mM; DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 1 mM; entity_3 1 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 8.9; 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-1H COSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 800 MHz