BMRB Entry 36172

Name: NMR structure of p75NTR transmembrane domain in complex with NSC49652
Published: 2019-03-11

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PDB ID: 5zgg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36172
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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 p75NTR transmembrane domain in complex with NSC49652

Deposition date:

2018-03-08

Original release date:

2019-03-11

Authors:

Lin, Z.; Ibanez, C.

Citation:

Citation: Goh, Eddy; Lin, Zhi; Ahn, Bo Young; Lopes-Rodrigues, Vanessa; Dang, Ngoc Ha; Salim, Shuhailah; Berger, Bryan; Dymock, Brian; Senger, Donna; Ibanez, Carlos. "A Small Molecule Targeting the Transmembrane Domain of Death Receptor p75NTR Induces Melanoma Cell Death and Reduces Tumor Growth" Cell Chem. Biol. 25, 1485-1494 (2018).
PubMed: 30293939

Assembly members:

Assembly members:
Tumor necrosis factor receptor superfamily member 16, polymer, 34 residues, 3715.347 Da.
(2E)-1-(2-hydroxyphenyl)-3-(pyridin-3-yl)prop-2-en-1-one, non-polymer, 225.243 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: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Tumor necrosis factor receptor superfamily member 16: TRGTTDNLIPVYCSILAAVV VGLVAYIAFKRWNS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	117
15N chemical shifts	35
1H chemical shifts	242

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1
3	entity_9F6	2

Entities:

Entity 1, entity_1, 1 34 residues - 3715.347 Da.

1

THR

ARG

GLY

THR

ASP

ASN

LEU

ILE

PRO

2

VAL

TYR

CYS

SER

ILE

LEU

ALA

VAL

3

VAL

GLY

LEU

VAL

ALA

TYR

ILE

ALA

PHE

LYS

4

ARG

TRP

ASN

SER

Entity 2, entity_9F6 - C14 H11 N O2 - 225.243 Da.

1

9F6

Samples:

sample_1: p75NTR TMD, [U-99% 13C; U-99% 15N], 0.8 mM; NSC49652 3.9 mM; DMSO, [U-99.9% 2H], 5%; DPC, [U-98% 2H], 200 mM; H2O 90%; D2O, [U-2H], 10%; phosphate buffer 5 mM

sample_conditions_1: ionic strength: 5 mM; pH: 6.0; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D TOCSY	sample_1	isotropic	sample_conditions_1
3D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C filtered NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 800 MHz

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