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9qb6

;Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment H02 and CX-4945 (Silmitasertib) ;

Method: X-RAY DIFFRACTION D_max: 70.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qb6
deposition_date	2025-02-28
last_revision	2026-01-14
title	;Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment H02 and CX-4945 (Silmitasertib) ;
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	21.62 Å
rg_electron	20.45 Å
i0	25330200.00
molecular_weight	39580.0 kDa
excluded_volume	49934 Å³
envelope_volume	56985 Å³
shell_volume	23026 Å³
envelope_diameter	70.1 Å
shell_rg	27.47 Å
envelope_rg	20.72 Å
shape_rg	20.45 Å
total_rg	21.34 Å
total_atoms	5565
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	70.3 Å
rg_real	21.53 Å
rg_real_error	0.39 Å
i0_real	2.5330e+07
i0_real_error	3.4460e+05
rg_reciprocal	21.55 Å
i0_reciprocal	25330000.0000
total_estimate	0.8905
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.238
kurtosis	-0.381
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	8051000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	5979

MGSSHHHHHHSSGLVPRGSHMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	3-cyclopentyl-1-(piperazin-1-yl)propan-1-one
formula_weight	210.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
formula_weight	349.8 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	296

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6. Citations (1)

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length_a	46.453 Å
length_b	47.708 Å
length_c	50.496 Å
angle_alpha	66.62 °
angle_beta	89.80 °
angle_gamma	88.43 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.050 Å
resolution_low	46.350 Å
r_factor	0.1269
r_work	0.1267
r_free	0.1439

fit	/app/data/saxs_computation/qb/9qb6/9qb6.fit
pddf	/app/data/pr_computation/qb/9qb6/9qb6.pr.out
profile	/app/data/saxs_computation/qb/9qb6/9qb6.dat

;Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment H02 and CX-4945 (Silmitasertib) ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction