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9ymt

Staphylococcus aureus serine/threonine kinase Stk1 with inhibitor GW779439X

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ymt
deposition_date	2025-10-10
last_revision	2026-03-11
title	Staphylococcus aureus serine/threonine kinase Stk1 with inhibitor GW779439X
keywords	Kinase, Inhibitor, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.17 Å
rg_electron	19.45 Å
i0	33921600.00
molecular_weight	29980.0 kDa
excluded_volume	28921 Å³
envelope_volume	45931 Å³
shell_volume	19954 Å³
envelope_diameter	68.8 Å
shell_rg	25.62 Å
envelope_rg	19.70 Å
shape_rg	19.42 Å
total_rg	20.11 Å
total_atoms	2267
n_residues	273
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	67.6 Å
rg_real	20.15 Å
rg_real_error	0.49 Å
i0_real	3.3920e+07
i0_real_error	4.3140e+05
rg_reciprocal	20.15 Å
i0_reciprocal	33920000.0000
total_estimate	0.8760
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.363
kurtosis	-0.211
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	7581000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Serine/Threonine Kinase
formula_weight	33053.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2350

GSHMIGKIINERYKIVDKLGGGGMSTVYLAEDTILNIKVAIKAIFIPPREKEETLKRFEREVHNSSQLSHQNIVSMIDVDEEDDCYYLVMEYIEGPTLSEYIESHGPLSVDTAINFTNQILDGIKHAHDMRIVHRDIKPQNILIDSNKTLKIFDFGIAKALSETSLTQTNHVLGTVQYFSPEQAKGEATDECTDIYSIGIVLYEMLVGEPPFNGETAVSIAIKHIQDSVPNVTTDVRKDIPQSLSNVILRATEKDKANRYKTIQEMKDDLSSVLHENRANEDVYELDKMKTIA

Source

organism	Staphylococcus aureus subsp. aureus N315
ncbi_taxonomy_id	158879
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	(4M)-N-[4-(4-methylpiperazin-1-yl)-3-(trifluoromethyl)phenyl]-4-[(8R)-pyrazolo[1,5-b]pyridazin-3-yl]pyrimidin-2-amine
formula_weight	454.5 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	BENZAMIDINE
formula_weight	120.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	72

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6. Citations (1)

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length_a	100.792 Å
length_b	100.792 Å
length_c	91.698 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	2.070 Å
resolution_low	45.080 Å
r_factor	0.2162
r_work	0.2128
r_free	0.2495

fit	/app/data/saxs_computation/ym/9ymt/9ymt.fit
pddf	/app/data/pr_computation/ym/9ymt/9ymt.pr.out
profile	/app/data/saxs_computation/ym/9ymt/9ymt.dat