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9vrs

Crystal structure of human PTPN2 with inhibitor WS19

Method: X-RAY DIFFRACTION D_max: 94.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vrs
deposition_date	2025-07-07
last_revision	2025-12-17
title	Crystal structure of human PTPN2 with inhibitor WS19
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	28.19 Å
rg_electron	27.61 Å
i0	141423000.00
molecular_weight	62580.0 kDa
excluded_volume	60345 Å³
envelope_volume	105550 Å³
shell_volume	31942 Å³
envelope_diameter	98.3 Å
shell_rg	34.70 Å
envelope_rg	27.43 Å
shape_rg	27.59 Å
total_rg	28.16 Å
total_atoms	4733
n_residues	577
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	94.5 Å
rg_real	28.18 Å
rg_real_error	0.67 Å
i0_real	1.4140e+08
i0_real_error	2.0730e+06
rg_reciprocal	28.19 Å
i0_reciprocal	141400000.0000
total_estimate	0.8869
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.7 Å
skewness	0.295
kurtosis	-0.527
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	28440000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.988

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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	4976

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-6-oxidanyl-4-(4,5,6,7-tetrahydropyrazolo[1,5-a]pyridin-3-yl)phenyl]-1,1-bis(oxidanylidene)-1,2,5-thiadiazolidin-3-one ;
formula_weight	366.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	243

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6. Citations (1)

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length_a	60.000 Å
length_b	78.810 Å
length_c	80.880 Å
angle_alpha	90.00 °
angle_beta	111.73 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	27.870 Å
r_factor	0.1848
r_work	0.1838
r_free	0.2168

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

Crystal structure of human PTPN2 with inhibitor WS19

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