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9uzt

Crystal structure of human PTPN2 with inhibitor K-38

Method: X-RAY DIFFRACTION D_max: 66.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uzt
deposition_date	2025-05-16
last_revision	2025-12-17
title	Crystal structure of human PTPN2 with inhibitor K-38
keywords	PTPN2, inhibitor, Tumor Immunity, IMMUNE SYSTEM; IMMUNE SYSTEM
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	19.71 Å
rg_electron	18.82 Å
i0	36483900.00
molecular_weight	31003.0 kDa
excluded_volume	29876 Å³
envelope_volume	47239 Å³
shell_volume	20674 Å³
envelope_diameter	67.2 Å
shell_rg	25.61 Å
envelope_rg	19.30 Å
shape_rg	18.81 Å
total_rg	19.54 Å
total_atoms	2345
n_residues	283
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	66.3 Å
rg_real	19.64 Å
rg_real_error	0.35 Å
i0_real	3.6480e+07
i0_real_error	4.0580e+05
rg_reciprocal	19.65 Å
i0_reciprocal	36480000.0000
total_estimate	0.7355
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.3 Å
skewness	0.319
kurtosis	-0.201
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	9281000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.994; Smooth: 0.955

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Tyrosine-protein phosphatase non-receptor type 2
formula_weight	34932.6 kDa
ec_number	3.1.3.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	2497

PLGSPWGSIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKED

Source

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

Entity 2 non-polymer

description	;~{N}-cycloheptyl-4-[3-fluoranyl-5-oxidanyl-4-[1,1,4-tris(oxidanylidene)-1,2,5-thiadiazolidin-2-yl]phenyl]-1~{H}-imidazole-2-carboxamide ;
formula_weight	451.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	152

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6. Citations (1)

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length_a	94.950 Å
length_b	94.950 Å
length_c	100.514 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.170 Å
resolution_low	42.880 Å
r_factor	0.1840
r_work	0.1819
r_free	0.2126

fit	/app/data/saxs_computation/uz/9uzt/9uzt.fit
pddf	/app/data/pr_computation/uz/9uzt/9uzt.pr.out
profile	/app/data/saxs_computation/uz/9uzt/9uzt.dat

Crystal structure of human PTPN2 with inhibitor K-38

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