← Back to search

9ydm

Targeting PTPN22 at non-orthosteric binding sites - a fragment approach

Method: X-RAY DIFFRACTION D_max: 100.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ydm
deposition_date	2025-09-22
title	Targeting PTPN22 at non-orthosteric binding sites - a fragment approach
keywords	non-receptor protein tyrosine phosphatase, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.22 Å
rg_electron	29.67 Å
i0	76014000.00
molecular_weight	70145.0 kDa
excluded_volume	88152 Å³
envelope_volume	109430 Å³
shell_volume	31563 Å³
envelope_diameter	105.2 Å
shell_rg	35.79 Å
envelope_rg	30.05 Å
shape_rg	29.65 Å
total_rg	30.33 Å
total_atoms	9729
n_residues	599
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

▼

3. P(r) Analysis (GNOM)

dmax	100.4 Å
rg_real	30.37 Å
rg_real_error	0.89 Å
i0_real	7.6010e+07
i0_real_error	1.2910e+06
rg_reciprocal	30.31 Å
i0_reciprocal	76010000.0000
total_estimate	0.8680
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.452
kurtosis	-0.422
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	24780000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.873

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Tyrosine-protein phosphatase non-receptor type 22
formula_weight	37755.1 kDa
ec_number	3.1.3.48
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10122

HHHHHHGENLYFQGSMDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNSETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGGNS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ETHANOL
formula_weight	46.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	N-(3-methyl-1H-pyrazol-5-yl)-3-phenylpropanamide
formula_weight	229.3 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	377

▶

6. Citations (1)

▶

length_a	60.209 Å
length_b	48.640 Å
length_c	120.290 Å
angle_alpha	90.00 °
angle_beta	102.88 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.990 Å
resolution_low	57.910 Å
r_factor	0.2350
r_work	0.2329
r_free	0.2757

fit	/app/data/saxs_computation/yd/9ydm/9ydm.fit
pddf	/app/data/pr_computation/yd/9ydm/9ydm.pr.out
profile	/app/data/saxs_computation/yd/9ydm/9ydm.dat