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9rdy

Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F024

Method: X-RAY DIFFRACTION D_max: 67.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rdy
deposition_date	2025-06-03
title	Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F024
keywords	serine-threonine kinase, small molecules, ligand binding, fragment-based drug discovery, 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	21.50 Å
rg_electron	20.40 Å
i0	48369100.00
molecular_weight	36756.0 kDa
excluded_volume	35909 Å³
envelope_volume	59445 Å³
shell_volume	23849 Å³
envelope_diameter	69.8 Å
shell_rg	27.35 Å
envelope_rg	20.52 Å
shape_rg	20.34 Å
total_rg	21.16 Å
total_atoms	2786
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

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3. P(r) Analysis (GNOM)

dmax	67.2 Å
rg_real	21.36 Å
rg_real_error	0.30 Å
i0_real	4.8370e+07
i0_real_error	6.2320e+05
rg_reciprocal	21.39 Å
i0_reciprocal	48370000.0000
total_estimate	0.9017
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.175
kurtosis	-0.430
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	10170000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	3118

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	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	(1~{S},4~{R})-4-(3,5-dimethyl-1~{H}-pyrazol-4-yl)cyclopent-2-en-1-ol
formula_weight	178.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	253

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6. Citations (1)

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length_a	52.594 Å
length_b	72.537 Å
length_c	99.759 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	1.500 Å
resolution_low	24.940 Å
r_factor	0.1837
r_work	0.1825
r_free	0.2063

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

Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F024

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