BMRB Entry 34653

Name: NMR structure of a peptide deriving from SARS-CoV-2 Lineages P.1 and B.1.351 S RBD 482-506 fragment in HFIP/H2O
Published: 2022-07-21

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PDB ID: 7p5s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34653
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of a peptide deriving from SARS-CoV-2 Lineages P.1 and B.1.351 S RBD 482-506 fragment in HFIP/H2O PubMed: 36406731

Deposition date: 2021-07-14 Original release date: 2022-07-21

Authors: Santoro, A.; Buonocore, M.; Grimaldi, M.; D'Ursi, A.M.

Citation: Buonocore, Michela; Santoro, Angelo; Grimaldi, Manuela; Covelli, Verdiana; Firoznezhad, Mohammad; Rodriquez, Manuela; Santin, Matteo; D'Ursi, Anna Maria. "Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site" Heliyon 8, e11568-e11568 (2022).

Assembly members:
entity_1, polymer, 25 residues, 2822.133 Da.

Natural source: Common Name: 2019-nCoV, SARS-CoV-2 Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GVKGFNCYFPLQSYGFQPTY GVGYQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	54
1H chemical shifts	153

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 25 residues - 2822.133 Da.

1

GLY

VAL

LYS

GLY

PHE

ASN

CYS

TYR

PHE

PRO

2

LEU

GLN

SER

TYR

GLY

PHE

GLN

PRO

THR

TYR

3

GLY

VAL

GLY

TYR

GLN

Samples:

sample_1: SMIMIC-BRASA 2.5 mM; Hexafluoroisopropanol 50 % v/v; H2O 40 % v/v; D2O, [U-100% 2H], 10 % v/v

sample_conditions_1: ionic strength: 0 Not defined; pH: 2.5; 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-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

NMRFAM-SPARKY, Lee - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

TALOS-N, Bax - refinement

NMR spectrometers:

Bruker AVANCE II 500 MHz