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9zmf

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 10

Method: X-RAY DIFFRACTION D_max: 69.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zmf
deposition_date	2025-12-10
last_revision	2026-05-27
title	Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 10
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	19.91 Å
rg_electron	18.98 Å
i0	38935700.00
molecular_weight	31897.0 kDa
excluded_volume	30641 Å³
envelope_volume	48688 Å³
shell_volume	21067 Å³
envelope_diameter	70.2 Å
shell_rg	25.80 Å
envelope_rg	19.41 Å
shape_rg	18.96 Å
total_rg	19.69 Å
total_atoms	2401
n_residues	291
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	69.1 Å
rg_real	19.81 Å
rg_real_error	0.37 Å
i0_real	3.8940e+07
i0_real_error	4.8970e+05
rg_reciprocal	19.83 Å
i0_reciprocal	38940000.0000
total_estimate	0.8589
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.3 Å
skewness	0.265
kurtosis	-0.293
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0002
highest_alpha	8434000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 1.000

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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	2488

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-5-carbamoyl-1-benzothiophen-2-yl)di(fluoro)methyl]phosphonic acid
formula_weight	386.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	87

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6. Citations (1)

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length_a	89.328 Å
length_b	89.328 Å
length_c	106.516 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	2.510 Å
resolution_low	23.210 Å
r_factor	0.2271
r_work	0.2261
r_free	0.2465

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

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 10

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