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9zkg

VRK1 in complex with the inhibitor MP-60

Method: X-RAY DIFFRACTION D_max: 132.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zkg
deposition_date	2025-12-06
title	VRK1 in complex with the inhibitor MP-60
keywords	PROTEIN KINASE, INHIBITOR, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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	39.06 Å
rg_electron	38.84 Å
i0	608644000.00
molecular_weight	134120.0 kDa
excluded_volume	129660 Å³
envelope_volume	233400 Å³
shell_volume	50524 Å³
envelope_diameter	142.0 Å
shell_rg	44.03 Å
envelope_rg	38.38 Å
shape_rg	38.83 Å
total_rg	39.07 Å
total_atoms	10151
n_residues	1269
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	132.9 Å
rg_real	39.13 Å
rg_real_error	1.24 Å
i0_real	6.0860e+08
i0_real_error	1.2040e+07
rg_reciprocal	39.09 Å
i0_reciprocal	608600000.0000
total_estimate	0.8732
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.8 Å
skewness	0.358
kurtosis	-0.239
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	51340000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.817

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Serine/threonine-protein kinase VRK1
formula_weight	41138.1 kDa
ec_number	2.7.11.1
mutation	M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10764

SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE

Source

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

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	9

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	7

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	ACETONE
formula_weight	58.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	2-(2-azanylethanoylamino)ethanoic acid
formula_weight	132.1 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	(5Z)-3-butyl-5-[(3,5-dichloro-4-hydroxyphenyl)methylidene]-1,3-thiazolidine-2,4-dione
formula_weight	346.2 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	539

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6. Citations (1)

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length_a	91.460 Å
length_b	95.930 Å
length_c	191.830 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.060 Å
resolution_low	47.970 Å
r_factor	0.1825
r_work	0.1807
r_free	0.2159

fit	/app/data/saxs_computation/zk/9zkg/9zkg.fit
pddf	/app/data/pr_computation/zk/9zkg/9zkg.pr.out
profile	/app/data/saxs_computation/zk/9zkg/9zkg.dat