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9vrr

Crystal structure of human PTPN2 with inhibitor WS3

Method: X-RAY DIFFRACTION D_max: 91.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vrr
deposition_date	2025-07-07
last_revision	2025-12-17
title	Crystal structure of human PTPN2 with inhibitor WS3
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	28.26 Å
rg_electron	27.67 Å
i0	141492000.00
molecular_weight	62642.0 kDa
excluded_volume	60434 Å³
envelope_volume	106970 Å³
shell_volume	32236 Å³
envelope_diameter	99.0 Å
shell_rg	34.83 Å
envelope_rg	27.55 Å
shape_rg	27.65 Å
total_rg	28.23 Å
total_atoms	4738
n_residues	578
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	91.8 Å
rg_real	28.24 Å
rg_real_error	0.59 Å
i0_real	1.4150e+08
i0_real_error	2.0350e+06
rg_reciprocal	28.25 Å
i0_reciprocal	141500000.0000
total_estimate	0.8976
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.5 Å
skewness	0.298
kurtosis	-0.524
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	27440000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.984

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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	34989.6 kDa
ec_number	3.1.3.48
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	4950

GPLGSPWGSIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKED

Source

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

Entity 2 non-polymer

description	5-[2-fluoranyl-4-[1-(3-methylbutyl)azetidin-3-yl]-6-oxidanyl-phenyl]-1,1-bis(oxidanylidene)-1,2,5-thiadiazolidin-3-one
formula_weight	371.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	212

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6. Citations (1)

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length_a	59.800 Å
length_b	79.190 Å
length_c	81.131 Å
angle_alpha	90.00 °
angle_beta	111.40 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.950 Å
resolution_low	27.840 Å
r_factor	0.1931
r_work	0.1920
r_free	0.2219

fit	/app/data/saxs_computation/vr/9vrr/9vrr.fit
pddf	/app/data/pr_computation/vr/9vrr/9vrr.pr.out
profile	/app/data/saxs_computation/vr/9vrr/9vrr.dat

Crystal structure of human PTPN2 with inhibitor WS3

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