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9r59

Crystal structure of MAPKAPK2 with a covalent compound GCL334 targeting lysine

Method: X-RAY DIFFRACTION D_max: 66.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r59
deposition_date	2025-05-08
title	Crystal structure of MAPKAPK2 with a covalent compound GCL334 targeting lysine
keywords	kinase, covalent inhibitor, lysine, MAPKAPK2, 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	20.67 Å
rg_electron	19.91 Å
i0	33968700.00
molecular_weight	30077.0 kDa
excluded_volume	29088 Å³
envelope_volume	47246 Å³
shell_volume	20080 Å³
envelope_diameter	66.2 Å
shell_rg	26.05 Å
envelope_rg	20.16 Å
shape_rg	19.89 Å
total_rg	20.55 Å
total_atoms	2266
n_residues	281
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	66.7 Å
rg_real	20.65 Å
rg_real_error	0.41 Å
i0_real	3.3970e+07
i0_real_error	4.1800e+05
rg_reciprocal	20.65 Å
i0_reciprocal	33970000.0000
total_estimate	0.8893
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.337
kurtosis	-0.358
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	6865000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	MAP kinase-activated protein kinase 2
formula_weight	36903.7 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2278

GHMVKSGLQIKKNAIIDDYKVTSQVLGLGINGKVLQIFNKRTQEKFALKMLQDCPKARREVELHWRASQCPHIVRIVDVYENLYAGRKCLLIVMECLDGGELFSRIQDRGDQAFTEREASEIMKSIGEAIQYLHSINIAHRDVKPENLLYTSKRPNAILKLTDFGFAKETTGHNSLTTPCYTPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQYEFPNPEWSEVSEEVKMLIRNLLKTEPTQRMTITEFMNHPWIMQSTKVPQTPLHTSRVLKEDKERWEDVKEEMTSALATMR

Source

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

Entity 2 non-polymer

description	;5-[3-[bis(oxidanyl)-$l^{3}-sulfanyl]oxy-4-chloranyl-phenyl]-~{N}-(4-piperazin-1-ylphenyl)-~{N}-(pyridin-2-ylmethyl)furan-2-carboxamide ;
formula_weight	571.0 kDa
src_method	man
entity_count	1

Source

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

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (1)

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length_a	102.745 Å
length_b	102.745 Å
length_c	167.683 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63 2 2
int_tables_number	182
crystal_system	—

resolution	3.000 Å
resolution_low	49.170 Å
r_factor	0.2021
r_work	0.2006
r_free	0.2290

fit	/app/data/saxs_computation/r5/9r59/9r59.fit
pddf	/app/data/pr_computation/r5/9r59/9r59.pr.out
profile	/app/data/saxs_computation/r5/9r59/9r59.dat

Crystal structure of MAPKAPK2 with a covalent compound GCL334 targeting lysine

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)