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9zme

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 2

Method: X-RAY DIFFRACTION D_max: 68.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zme
deposition_date	2025-12-10
last_revision	2026-05-27
title	Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 2
keywords	HYDROLASE-INHIBITOR complex, PTP1B; HYDROLASE/INHIBITOR
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	20.12 Å
rg_electron	19.24 Å
i0	41231200.00
molecular_weight	32996.0 kDa
excluded_volume	31771 Å³
envelope_volume	50384 Å³
shell_volume	21488 Å³
envelope_diameter	69.7 Å
shell_rg	26.09 Å
envelope_rg	19.75 Å
shape_rg	19.23 Å
total_rg	19.94 Å
total_atoms	2485
n_residues	301
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	68.2 Å
rg_real	20.05 Å
rg_real_error	0.38 Å
i0_real	4.1230e+07
i0_real_error	4.7710e+05
rg_reciprocal	20.06 Å
i0_reciprocal	41230000.0000
total_estimate	0.8694
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.2 Å
skewness	0.290
kurtosis	-0.243
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	8875000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.987

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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 1
formula_weight	38883.2 kDa
ec_number	3.1.3.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2733

MDYKDDDDKLEFMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN

Source

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

Entity 2 non-polymer

description	{[3-bromo-7-(3-hydroxy-3-methylbutoxy)naphthalen-2-yl]di(fluoro)methyl}phosphonic acid
formula_weight	439.2 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	248

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6. Citations (1)

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length_a	88.254 Å
length_b	88.254 Å
length_c	103.843 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	1.730 Å
resolution_low	25.240 Å
r_factor	0.1856
r_work	0.1847
r_free	0.2029

fit	/app/data/saxs_computation/zm/9zme/9zme.fit
pddf	/app/data/pr_computation/zm/9zme/9zme.pr.out
profile	/app/data/saxs_computation/zm/9zme/9zme.dat

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 2

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