← Back to search

9rdz

Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F030

Method: X-RAY DIFFRACTION D_max: 67.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rdz
deposition_date	2025-06-03
title	Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F030
keywords	serine-threonine kinase, small molecules, ligand binding, fragment-based drug discovery, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	21.41 Å
rg_electron	20.32 Å
i0	50702400.00
molecular_weight	37639.0 kDa
excluded_volume	36745 Å³
envelope_volume	59796 Å³
shell_volume	24020 Å³
envelope_diameter	69.5 Å
shell_rg	27.39 Å
envelope_rg	20.47 Å
shape_rg	20.24 Å
total_rg	21.12 Å
total_atoms	2841
n_residues	336
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

▼

3. P(r) Analysis (GNOM)

dmax	67.7 Å
rg_real	21.27 Å
rg_real_error	0.30 Å
i0_real	5.0700e+07
i0_real_error	6.4290e+05
rg_reciprocal	21.30 Å
i0_reciprocal	50700000.0000
total_estimate	0.8973
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.9 Å
skewness	0.179
kurtosis	-0.415
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	10310000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.999

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	cAMP-dependent protein kinase catalytic subunit alpha
formula_weight	41113.8 kDa
ec_number	2.7.11.11
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3226

GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF

Source

organism	Cricetulus griseus
common_name	Chinese hamster
ncbi_taxonomy_id	10029
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	[(3~{S},3~{a}~{R},6~{R},6~{a}~{S})-3-azanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-6-yl] ~{N}-phenylcarbamate
formula_weight	264.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	nat
entity_count	7

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	251

▶

6. Citations (1)

▶

length_a	52.385 Å
length_b	72.049 Å
length_c	98.384 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.640 Å
resolution_low	42.370 Å
r_factor	0.1805
r_work	0.1788
r_free	0.2122

fit	/app/data/saxs_computation/rd/9rdz/9rdz.fit
pddf	/app/data/pr_computation/rd/9rdz/9rdz.pr.out
profile	/app/data/saxs_computation/rd/9rdz/9rdz.dat