BMRB Entry 31143

Name: Wheat Germ Agglutinin (WGA) domain D
Published: 2024-05-30

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PDB ID: 8vu8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31143
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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:

Wheat Germ Agglutinin (WGA) domain D

Deposition date:

2024-01-29

Original release date:

2024-05-30

Authors:

Titaux-Delgado, G.; del Rio-Portilla, F.; Garcia-Hernandez, E.

Citation:

Citation: Medrano-Cerano, Jorge Luis; Cofas-Vargas, Luis Fernando; Leyva, Eduardo; Rauda-Ceja, Jesus Antonio; Calderon-Vargas, Mateo; Cano-Sanchez, Patricia; Titaux-Delgado, Gustavo; Melchor-Meneses, Carolina Monserrath; Hernandez-Arana, Andres; Del Rio-Portilla, Federico; Garcia-Hernandez, Enrique. "Decoding the mechanism governing the structural stability of wheat germ agglutinin and its isolated domains: A combined calorimetric, NMR, and MD simulation study" Protein Sci. 33, e5020-e5020 (2024).
PubMed: 38747397

Assembly members:

Assembly members:
entity_1, polymer, 43 residues, 4197.678 Da.

Natural source:

Natural source: Common Name: bread wheat Taxonomy ID: 4565 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Triticum aestivum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: DKPCGKDAGGRVCTNNYCCS KWGSCGIGPGYCGAGCQSGG CDG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	204

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 43 residues - 4197.678 Da.

1

ASP

LYS

PRO

CYS

GLY

LYS

ASP

ALA

GLY

2

ARG

VAL

CYS

THR

ASN

TYR

CYS

SER

3

LYS

TRP

GLY

SER

CYS

GLY

ILE

GLY

PRO

GLY

4

TYR

CYS

GLY

ALA

GLY

CYS

GLN

SER

GLY

5

CYS

ASP

GLY

Samples:

sample_1: WGA_domD 1 mM; Phosphate buffer 30 mM

sample_conditions_1: ionic strength: 0.116 M; pH: 4.74; pressure: 1 atm; temperature: 298 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-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

CARA v1.8, Keller and Wuthrich - chemical shift assignment

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure calculation

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

CARA v2.1, Keller and Wuthrich - peak picking

NMR spectrometers:

Bruker AVANCE III 700 MHz