BMRB Entry 30605
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30605
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Title: SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH1/AA] AND PLASMINOGEN KRINGLE 2
Deposition date: 2019-04-26 Original release date: 2019-07-18
Authors: Yuan, Y.; Castellino, F.
Citation: Yuan, Y.; Ploplis, V.; Lee, S.; Castellino, F.. "Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcal pyogenes" . ., .-..
Assembly members:
entity_1, polymer, 87 residues, 10166.340 Da.
entity_2, polymer, 52 residues, 6020.606 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Komagataella pastoris
Entity Sequences (FASTA):
entity_1: YVEFSEECMHGSGENYDGKI
SKTMSGLECQAWDSQSPHAH
GYIPSKFPNKNLKKNYCRNP
DRDLRPWCFTTDPNKRWEYC
DIPRCAA
entity_2: GSVEKLTADAELQRLKNEAA
EEAELERLKSERHDHDKKEA
ERKALEDKLADY
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 569 |
| 15N chemical shifts | 146 |
| 1H chemical shifts | 855 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 87 residues - 10166.340 Da.
| 1 | TYR | VAL | GLU | PHE | SER | GLU | GLU | CYS | MET | HIS | ||||
| 2 | GLY | SER | GLY | GLU | ASN | TYR | ASP | GLY | LYS | ILE | ||||
| 3 | SER | LYS | THR | MET | SER | GLY | LEU | GLU | CYS | GLN | ||||
| 4 | ALA | TRP | ASP | SER | GLN | SER | PRO | HIS | ALA | HIS | ||||
| 5 | GLY | TYR | ILE | PRO | SER | LYS | PHE | PRO | ASN | LYS | ||||
| 6 | ASN | LEU | LYS | LYS | ASN | TYR | CYS | ARG | ASN | PRO | ||||
| 7 | ASP | ARG | ASP | LEU | ARG | PRO | TRP | CYS | PHE | THR | ||||
| 8 | THR | ASP | PRO | ASN | LYS | ARG | TRP | GLU | TYR | CYS | ||||
| 9 | ASP | ILE | PRO | ARG | CYS | ALA | ALA |
Entity 2, entity_2 52 residues - 6020.606 Da.
| 1 | GLY | SER | VAL | GLU | LYS | LEU | THR | ALA | ASP | ALA | ||||
| 2 | GLU | LEU | GLN | ARG | LEU | LYS | ASN | GLU | ALA | ALA | ||||
| 3 | GLU | GLU | ALA | GLU | LEU | GLU | ARG | LEU | LYS | SER | ||||
| 4 | GLU | ARG | HIS | ASP | HIS | ASP | LYS | LYS | GLU | ALA | ||||
| 5 | GLU | ARG | LYS | ALA | LEU | GLU | ASP | LYS | LEU | ALA | ||||
| 6 | ASP | TYR |
Samples:
sample_1: plasminogen kringle 2, [U-99% 13C; U-99% 15N], 1.0 mM; VEK50[RH1/AA] 1.0 mM; Bis-Tris-d19, [U-2H], 20 mM; DSS 2 ug/mL; sodium azide 2 ug/mL
sample_2: plasminogen kringle 2 1 mM; VEK50[RH1/AA], [U-99% 13C; U-99% 15N], 1 mM; Bis-Tris-d19, [U-2H], 20 mM; DSS 2 ug/mL; sodium azide 2 ug/mL
sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
Software:
TopSpin, Bruker Biospin - collection, processing
Sparky, Goddard - chemical shift assignment
CS-ROSETTA, Shen, Vernon, Baker and Bax - structure calculation
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
HADDOCK, Bonvin - refinement
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