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9qri

Protein Kinase CK2 and bivalent inhibitors

Method: X-RAY DIFFRACTION D_max: 114.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qri
deposition_date	2025-04-03
last_revision	2025-07-30
title	Protein Kinase CK2 and bivalent inhibitors
keywords	Protein kinase inhibitor bivalent aD pocket, 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	32.12 Å
rg_electron	32.11 Å
i0	188788000.00
molecular_weight	73803.0 kDa
excluded_volume	71509 Å³
envelope_volume	121450 Å³
shell_volume	33302 Å³
envelope_diameter	122.2 Å
shell_rg	36.59 Å
envelope_rg	32.58 Å
shape_rg	32.11 Å
total_rg	32.37 Å
total_atoms	5586
n_residues	660
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	114.1 Å
rg_real	32.50 Å
rg_real_error	1.45 Å
i0_real	1.8880e+08
i0_real_error	3.7470e+06
rg_reciprocal	32.34 Å
i0_reciprocal	188800000.0000
total_estimate	0.8059
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.3 Å
skewness	0.605
kurtosis	-0.181
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	26180000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.617; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.716; Smooth: 0.910

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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	42799.6 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5617

MHHHHHHSSGVDLGTENLYFQSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	5-[4-[[4-[2-(3,4-dichlorophenyl)ethylamino]-4-oxidanylidene-butanoyl]amino]butylamino]benzo[c][2,6]naphthyridine-8-carboxylic acid
formula_weight	582.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	9

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

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6. Citations (1)

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length_a	127.136 Å
length_b	127.136 Å
length_c	124.999 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.350 Å
resolution_low	44.950 Å
r_factor	0.2016
r_work	0.1994
r_free	0.2435

fit	/app/data/saxs_computation/qr/9qri/9qri.fit
pddf	/app/data/pr_computation/qr/9qri/9qri.pr.out
profile	/app/data/saxs_computation/qr/9qri/9qri.dat

Protein Kinase CK2 and bivalent inhibitors

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