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9rdv

Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F005

Method: X-RAY DIFFRACTION D_max: 66.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rdv
deposition_date	2025-06-03
title	Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F005
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	21.31 Å
rg_electron	20.25 Å
i0	49978300.00
molecular_weight	37303.0 kDa
excluded_volume	36358 Å³
envelope_volume	58889 Å³
shell_volume	23725 Å³
envelope_diameter	69.1 Å
shell_rg	27.32 Å
envelope_rg	20.43 Å
shape_rg	20.19 Å
total_rg	21.01 Å
total_atoms	2824
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	66.6 Å
rg_real	21.18 Å
rg_real_error	0.29 Å
i0_real	4.9980e+07
i0_real_error	5.7190e+05
rg_reciprocal	21.20 Å
i0_reciprocal	49980000.0000
total_estimate	0.9006
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	65.6 Å
skewness	0.178
kurtosis	-0.422
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	10890000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.991

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4. Crystallography & Experiment

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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	3341

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	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	(3~{R},5~{S})-5-(3-pyrazin-2-yl-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol
formula_weight	233.2 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	324

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6. Citations (1)

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length_a	52.197 Å
length_b	71.793 Å
length_c	98.773 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	—

resolution	1.320 Å
resolution_low	24.690 Å
r_factor	0.1467
r_work	0.1452
r_free	0.1752

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