BMRB Entry 34378

Name: Structure of kiteplatinated dsDNA
Published: 2020-03-27

Click here to enlarge.

PDB ID: 6r14
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34378
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of kiteplatinated dsDNA

Deposition date:

2019-03-13

Original release date:

2020-03-27

Authors:

Margiotta, N.; Papadia, P.; Kubicek, K.; Krejcikova, M.; Gkionis, K.; Sponer, J.

Citation:

Citation: Krejcikova, M.; Papadia, P.; Gkionis, K.; Plats, J.; Petruzzella, E.; Savino, S.; Hoeschelle, J.; Natile, G.; Sponer, J.; Kubicek, K.; Margiotta, N.. "Structural characterization of kiteplatinated DNA" .

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3559.319 Da.
entity_2, polymer, 12 residues, 3768.453 Da.
entity_LN8, non-polymer, 380.173 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: CCTCAGGCCTCC
entity_2: GGAGGCCTGAGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	200

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_3	3

Entities:

Entity 1, entity_1 12 residues - 3559.319 Da.

1

DC

DT

DC

DA

DG

DC

DT

2

DC

Entity 2, entity_2 12 residues - 3768.453 Da.

1

DG

DA

DG

DC

DT

DG

DA

2

DG

Entity 3, entity_3 - C6 H14 Cl2 N2 Pt - 380.173 Da.

1

LN8

Samples:

sample_1: entity_1 1 mM; entity_2 1 mM; kiteplatin 1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

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

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 850 MHz
Bruker AVANCE III 950 MHz