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9qb9

;CK2, catalytic subunit alpha' (CSNK2A2 gene product) in complex with a heparin-derived trisaccharide and the ATP-competitive inhibitor 4w ;

Method: X-RAY DIFFRACTION D_max: 68.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qb9
deposition_date	2025-03-01
last_revision	2026-01-21
title	;CK2, catalytic subunit alpha' (CSNK2A2 gene product) in complex with a heparin-derived trisaccharide and the ATP-competitive inhibitor 4w ;
keywords	CK2, fragment-based screening, protein kinase, protein kinase CK2, casein kinase II, TRANSFERASE; TRANSFERASE
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	21.44 Å
rg_electron	20.30 Å
i0	27396500.00
molecular_weight	40401.0 kDa
excluded_volume	50556 Å³
envelope_volume	57550 Å³
shell_volume	23372 Å³
envelope_diameter	70.4 Å
shell_rg	27.38 Å
envelope_rg	20.56 Å
shape_rg	20.31 Å
total_rg	21.16 Å
total_atoms	5612
n_residues	327
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	68.9 Å
rg_real	21.33 Å
rg_real_error	0.45 Å
i0_real	2.7400e+07
i0_real_error	3.6160e+05
rg_reciprocal	21.35 Å
i0_reciprocal	27400000.0000
total_estimate	0.6159
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	26.3 Å
skewness	0.241
kurtosis	-0.308
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	7678000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 0.161; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;Casein kinase II subunit alpha' ;
formula_weight	43432.5 kDa
ec_number	2.7.11.1
mutation	C336S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5876

MGSSHHHHHHSSGLVPRGSHMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 branched

description	;2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ;
formula_weight	916.8 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	1,3-bis(bromanyl)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione
formula_weight	437.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	232

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6. Citations (1)

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length_a	46.537 Å
length_b	47.648 Å
length_c	50.438 Å
angle_alpha	66.53 °
angle_beta	89.38 °
angle_gamma	87.97 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.190 Å
resolution_low	43.680 Å
r_factor	0.1437
r_work	0.1431
r_free	0.1748

fit	/app/data/saxs_computation/qb/9qb9/9qb9.fit
pddf	/app/data/pr_computation/qb/9qb9/9qb9.pr.out
profile	/app/data/saxs_computation/qb/9qb9/9qb9.dat