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9qy7

Crystal Structure of 54e bound to CK2a

Method: X-RAY DIFFRACTION D_max: 69.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qy7
deposition_date	2025-04-17
title	Crystal Structure of 54e bound to CK2a
keywords	Fragment based drug discovery, kinase, Hydrolase; HYDROLASE
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	21.36 Å
rg_electron	20.43 Å
i0	49334800.00
molecular_weight	36806.0 kDa
excluded_volume	35729 Å³
envelope_volume	57388 Å³
shell_volume	23135 Å³
envelope_diameter	71.9 Å
shell_rg	27.37 Å
envelope_rg	20.70 Å
shape_rg	20.42 Å
total_rg	21.09 Å
total_atoms	2795
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	69.4 Å
rg_real	21.27 Å
rg_real_error	0.39 Å
i0_real	4.9330e+07
i0_real_error	6.2510e+05
rg_reciprocal	21.29 Å
i0_reciprocal	49340000.0000
total_estimate	0.8146
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.5 Å
skewness	0.240
kurtosis	-0.386
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	14410000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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	39031.4 kDa
ec_number	2.7.11.1
mutation	K74A, K75A, K76A, R21S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3190

SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	5-[2-[4-[[3-chloranyl-4-(trifluoromethyloxy)phenyl]methylamino]butoxy]ethylamino]benzo[c][2,6]naphthyridine-8-carboxamide
formula_weight	562.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	322

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6. Citations (1)

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length_a	58.295 Å
length_b	45.809 Å
length_c	63.064 Å
angle_alpha	90.00 °
angle_beta	111.39 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.390 Å
resolution_low	49.960 Å
r_factor	0.1830
r_work	0.1820
r_free	0.2080

fit	/app/data/saxs_computation/qy/9qy7/9qy7.fit
pddf	/app/data/pr_computation/qy/9qy7/9qy7.pr.out
profile	/app/data/saxs_computation/qy/9qy7/9qy7.dat

Crystal Structure of 54e bound to CK2a

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