BMRB Entry 30263

Name: Suboptimization of a glycine rich peptide allows the combinatorial space exploration for designing novel antimicrobial peptides
Published: 2018-03-01

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PDB ID: 5v1e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30263
MolProbity Validation Chart

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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:

Suboptimization of a glycine rich peptide allows the combinatorial space exploration for designing novel antimicrobial peptides

Deposition date:

2017-03-02

Original release date:

2018-03-01

Authors:

Alves, E.; Matos, C.

Citation:

Citation: Porto, William; Irazazabal, Luz; Alves, Eliane; Ribeiro, Suzana; Matos, Carolina; Pires, Allan; Fensterseifer, Isabel; Miranda, Vivian; Haney, Evan; Humblot, Vincent; Torres, Marcelo; Hancock, Robert; Liao, Luciano; Ladram, Ali; Lu, Timothy; de la Fuente-Nunez, Cesar; Franco, Octavio. "In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design" Nat. Commun. 9, 1490-1490 (2018).
PubMed: 29662055

Assembly members:

Assembly members:
entity_1, polymer, 21 residues, 2648.084 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: RQYMRQIEQALRYGYRISRR X

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	20
1H chemical shifts	108

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 21 residues - 2648.084 Da.

1

ARG

GLN

TYR

MET

ARG

GLN

ILE

GLU

GLN

ALA

2

LEU

ARG

TYR

GLY

TYR

ARG

ILE

SER

ARG

3

NH2

Samples:

sample_1: D2O 5%; H2O 90%; dodecylphosphocholine 100 mM; peptide 1 mM; sodium 2,2-dimethyl-2-silapentane-5-sulfonate 5%

sample_conditions_1: ionic strength: 0.01 M; pH: 4; pressure: 1 atm; temperature: 289 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:

Molmol, Koradi, Billeter and Wuthrich - data analysis

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

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

NMRView, Johnson, One Moon Scientific - data analysis

QUEEN, Nabuurs, Spronk, Krieger, Maassen, Vriend and Vuister - data analysis

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

X-PLOR NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AvanceIII 500 MHz