BMRB Entry 25597

Name: Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor
Published: 2015-09-10

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PDB ID: 2n2f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25597
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor PubMed: 26372966

Deposition date: 2015-05-06 Original release date: 2015-09-10

Authors: O'Connor, Casey; White, Kate; Doncescu, Nathalie; Didenko, Tatiana; Roth, Bryan; Czaplicki, Georges; Stevens, Raymond; Wuthrich, Kurt; Milon, Alain

Citation: O'Connor, Casey; White, Kate; Doncescu, Nathalie; Didenko, Tatiana; Roth, Bryan; Czaplicki, Georges; Stevens, Raymond; Wuthrich, Kurt; Milon, Alain. "NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor" Proc. Natl. Acad. Sci. U.S.A. 112, 11852-11857 (2015).

Assembly members:
Dynorphin_1-13, polymer, 13 residues, 1609.012 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
Dynorphin_1-13: YGGFLRRIRPKLK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	18
15N chemical shifts	18
1H chemical shifts	125

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 13 residues - 1609.012 Da.

1

TYR

GLY

PHE

LEU

ARG

ILE

ARG

PRO

2

LYS

LEU

LYS

Samples:

sample_1: Dynorphin 1-13, [U-15N-GFLI], 1 mM; potassium chloride 150 mM; MES, [U-2H], 40 mM; DSS 100 uM; KOR 10 uM; DDM 8 mM; CHS 1.6 mM; H2O 90%; D2O 10%

sample_2: Dynorphin 1-13, [U-15N-GFLIR; U-13C-R], 1 mM; potassium chloride 150 mM; MES, [U-2H], 40 mM; DSS 100 uM; KOR 10 uM; DDM 8 mM; CHS 1.6 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.1; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D HNCACB	sample_2	isotropic	sample_conditions_1
15N T1 T2 hetNOE	sample_1	isotropic	sample_conditions_1
15N T2	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN v3.2, Bruker Biospin - chemical shift assignment, peak picking, processing

AMBER v14, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - geometry optimization, structure solution

NMR spectrometers:

Bruker Avance III 800 MHz
Bruker Avance 800 MHz
Bruker Avance III 700 MHz
Bruker Avance III 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts