BMRB Entry 30271

Name: Solution structure of VKK38 bound to plasminogen kringle 2
Published: 2017-07-20

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PDB ID: 5v4u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30271
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of VKK38 bound to plasminogen kringle 2 PubMed: 28724633

Deposition date: 2017-03-10 Original release date: 2017-07-20

Authors: Yuan, Y.; Castellino, F.

Citation: Yuan, Yue; Zajicek, Jaroslav; Qiu, Cunjia; Chandrahas, Vishwanatha; Lee, Shaun; Ploplis, Victoria; Castellino, Francis. "Conformationally organized lysine isosteres in Streptococcus pyogenes M protein mediate direct high-affinity binding to human plasminogen" J. Biol. Chem. 292, 15016-15027 (2017).

Assembly members:
M protein, polymer, 40 residues, 4892.360 Da.

Natural source: Common Name: Streptococcus pyogenes Taxonomy ID: 1314 Superkingdom: Bacteria Kingdom: not available Genus/species: Streptococcus pyogenes

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

Entity Sequences (FASTA):
M protein: GSVKKLNDEVALERLKNERH VHDEEVELERLKNERHDHDY

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	133
15N chemical shifts	37
1H chemical shifts	170

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 40 residues - 4892.360 Da.

1	GLY	SER	VAL	LYS	LYS	LEU	ASN	ASP	GLU	VAL
2	ALA	LEU	GLU	ARG	LEU	LYS	ASN	GLU	ARG	HIS
3	VAL	HIS	ASP	GLU	GLU	VAL	GLU	LEU	GLU	ARG
4	LEU	LYS	ASN	GLU	ARG	HIS	ASP	HIS	ASP	TYR

Samples:

sample_1: BisTris-d19, [U-100% 2H], 20 mM; DSS 0.2 mM; EDTA 2 mM; Kringle2 2.5 mM; VKK38, [U-13C; U-15N], 1.0 mM; sodium azide 3 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 15N HSQC-NOESY	sample_1	isotropic	sample_conditions_1

Software:

TALOS-N, Cornilescu, Delaglio and Bax - data analysis

TOPSPIN, Bruker Biospin - chemical shift assignment, peak picking

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

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 800 MHz

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

1	GLY	SER	VAL	LYS	LYS	LEU	ASN	ASP	GLU	VAL
2	ALA	LEU	GLU	ARG	LEU	LYS	ASN	GLU	ARG	HIS
3	VAL	HIS	ASP	GLU	GLU	VAL	GLU	LEU	GLU	ARG
4	LEU	LYS	ASN	GLU	ARG	HIS	ASP	HIS	ASP	TYR

1	GLY	SER	VAL	LYS	LYS	LEU	ASN	ASP	GLU	VAL
2	ALA	LEU	GLU	ARG	LEU	LYS	ASN	GLU	ARG	HIS
3	VAL	HIS	ASP	GLU	GLU	VAL	GLU	LEU	GLU	ARG
4	LEU	LYS	ASN	GLU	ARG	HIS	ASP	HIS	ASP	TYR

1	GLY	SER	VAL	LYS	LYS	LEU	ASN	ASP	GLU	VAL
2	ALA	LEU	GLU	ARG	LEU	LYS	ASN	GLU	ARG	HIS
3	VAL	HIS	ASP	GLU	GLU	VAL	GLU	LEU	GLU	ARG
4	LEU	LYS	ASN	GLU	ARG	HIS	ASP	HIS	ASP	TYR