9ymt

Staphylococcus aureus serine/threonine kinase Stk1 with inhibitor GW779439X

Method: X-RAY DIFFRACTION Dmax: 67.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/Threonine Kinase

Staphylococcus aureus subsp. aureus N315

UniProt A0ABF7PGK0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–290 Not recorded A1CYJ (4M)-N-[4-(4-methylpiperazin-1-yl)-3-(trifluoromethyl)phenyl]-4-[(8R)-pyrazolo[1,5-b]pyridazin-3-yl]pyrimidin-2-amine × 3 BEN BENZAMIDINE × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;1 microlitre of 9 mg/mL Stk1 1-291, 5 mM MgCl2, 2% (w/v) benzamidine hydrochloride, 1 mM dithiothreitol, 20 mM HEPES pH 7.5, 150 mM NaCl and 2 mM GW779439X was mixed with 1 microlitre of reservoir solution: 80 mM 2-(N-morpholino)-ethanesulfonic acid, pH 6.0, 1.2 M sodium citrate, pH 7.0, 2% (w/v) benzamidine hydrochloride and 30 mM MgCl2 Resolution 2.07 Å R-free 0.249

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0ABF7PGK0_STAAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–293; UniProt 1–290

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9ymt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ymt
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9ymt
Deposition date deposition_date2025-10-10
最后修订 last_revision2026-03-11
Structure title titleStaphylococcus aureus serine/threonine kinase Stk1 with inhibitor GW779439X
Keywords keywordsKinase, Inhibitor, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.17
Radius of gyration Rg (electron density) rg_electron19.45
Forward intensity I(0) i033921600.00
Molecular weight molecular_weight29980.0 kDa
Excluded volume excluded_volume28921 ų
Envelope volume envelope_volume45931 ų
Hydration-shell volume shell_volume19954 ų
Envelope diameter envelope_diameter68.8
Shell Rg shell_rg25.62
Envelope Rg envelope_rg19.70
Shape Rg shape_rg19.42
Total Rg total_rg20.11
Total atoms total_atoms2267
Residues n_residues273
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.6
Rg (real space) rg_real20.15
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real3.3920e+07
I(0) uncertainty (real space) i0_real_error4.3140e+05
Rg (reciprocal space) rg_reciprocal20.15
I(0) (reciprocal space) i0_reciprocal33920000.0000
Solution quality estimate total_estimate0.8760
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1
Skewness Skewness skewness0.363
Kurtosis Kurtosis kurtosis-0.211
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7581000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.801; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)