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9r5d

;Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 4,6-dibromo-5,7-difluoro-1H-1,2,3-benzotriazole ;

Method: X-RAY DIFFRACTION D_max: 69.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r5d
deposition_date	2025-05-08
last_revision	2026-01-14
title	;Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 4,6-dibromo-5,7-difluoro-1H-1,2,3-benzotriazole ;
keywords	;human protein kinase CK2, human casein kinase 2, isoenzyme ck2alpha', CSNK2A2, 4, 6-dibromo-5, 7-difluoro-1H-1, 2, 3-benzotriazole, 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	21.80 Å
rg_electron	20.57 Å
i0	26099200.00
molecular_weight	39769.0 kDa
excluded_volume	50023 Å³
envelope_volume	58002 Å³
shell_volume	23277 Å³
envelope_diameter	70.9 Å
shell_rg	27.62 Å
envelope_rg	20.86 Å
shape_rg	20.57 Å
total_rg	21.52 Å
total_atoms	5573
n_residues	328
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	69.7 Å
rg_real	21.69 Å
rg_real_error	0.38 Å
i0_real	2.6100e+07
i0_real_error	3.3430e+05
rg_reciprocal	21.71 Å
i0_reciprocal	26100000.0000
total_estimate	0.8968
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.237
kurtosis	-0.376
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	8386000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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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	42879.9 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6012

MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	4,6-bis(bromanyl)-5,7-bis(fluoranyl)-1~{H}-benzotriazole
formula_weight	312.9 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	237

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6. Citations (2)

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length_a	46.629 Å
length_b	48.013 Å
length_c	50.942 Å
angle_alpha	113.31 °
angle_beta	89.99 °
angle_gamma	90.83 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.020 Å
resolution_low	46.620 Å
r_factor	0.1721
r_work	0.1711
r_free	0.1927

fit	/app/data/saxs_computation/r5/9r5d/9r5d.fit
pddf	/app/data/pr_computation/r5/9r5d/9r5d.pr.out
profile	/app/data/saxs_computation/r5/9r5d/9r5d.dat

;Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 4,6-dibromo-5,7-difluoro-1H-1,2,3-benzotriazole ;

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