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9r5z

Crystal structure of JAK3 with GCL258

Method: X-RAY DIFFRACTION D_max: 104.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r5z
deposition_date	2025-05-11
title	Crystal structure of JAK3 with GCL258
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	31.28 Å
rg_electron	31.25 Å
i0	109412000.00
molecular_weight	56034.0 kDa
excluded_volume	54421 Å³
envelope_volume	97560 Å³
shell_volume	27744 Å³
envelope_diameter	110.0 Å
shell_rg	35.59 Å
envelope_rg	31.38 Å
shape_rg	31.22 Å
total_rg	31.57 Å
total_atoms	4244
n_residues	533
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	104.8 Å
rg_real	31.62 Å
rg_real_error	0.95 Å
i0_real	1.0940e+08
i0_real_error	1.8260e+06
rg_reciprocal	31.48 Å
i0_reciprocal	109400000.0000
total_estimate	0.8050
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.7 Å
skewness	0.520
kurtosis	-0.435
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	11770000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.607; Smooth: 0.645

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Tyrosine-protein kinase JAK3
formula_weight	33417.3 kDa
ec_number	2.7.10.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4462

SMQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRALAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	3-(3-cyclohexyl-3,8,10-triazatricyclo[7.3.0.0^{2,6}]dodeca-1,4,6,8,11-pentaen-5-yl)benzenesulfonyl fluoride
formula_weight	397.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1-phenylurea
formula_weight	136.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	218

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6. Citations (1)

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length_a	41.850 Å
length_b	62.540 Å
length_c	101.197 Å
angle_alpha	90.00 °
angle_beta	93.71 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	41.800 Å
r_factor	0.2387
r_work	0.2359
r_free	0.2893

fit	/app/data/saxs_computation/r5/9r5z/9r5z.fit
pddf	/app/data/pr_computation/r5/9r5z/9r5z.pr.out
profile	/app/data/saxs_computation/r5/9r5z/9r5z.dat

Crystal structure of JAK3 with GCL258

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