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9szo

Crystal structure of the catalytic domain of USP7 in complex with Compound 13

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9szo
deposition_date	2025-10-15
title	Crystal structure of the catalytic domain of USP7 in complex with Compound 13
keywords	USP7 INHIBITOR COMPLEX, STRUCTURE-GUIDED DRUG DESIGN, CANCER, HYDROLASE; HYDROLASE
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	22.06 Å
rg_electron	21.18 Å
i0	45816900.00
molecular_weight	35158.0 kDa
excluded_volume	34006 Å³
envelope_volume	56825 Å³
shell_volume	22653 Å³
envelope_diameter	89.3 Å
shell_rg	27.84 Å
envelope_rg	22.03 Å
shape_rg	21.14 Å
total_rg	21.87 Å
total_atoms	2657
n_residues	321
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	85.0 Å
rg_real	22.11 Å
rg_real_error	0.75 Å
i0_real	4.5820e+07
i0_real_error	6.3050e+05
rg_reciprocal	22.10 Å
i0_reciprocal	45820000.0000
total_estimate	0.7890
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.4 Å
skewness	0.520
kurtosis	0.248
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	7080000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.507; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.777; Smooth: 0.955

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ubiquitin carboxyl-terminal hydrolase 7
formula_weight	41004.3 kDa
ec_number	3.4.19.12
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2695

KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRKERQE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;(43S,Z)-25-chloro-23-methyl-3-oxa-1(7,2)-thieno[3,2-b]pyridina-4(3,1)-piperidina-11(1,3)-imidazolidina-2(1,2)-benzenacyclododecaphan-7-ene-112,114-dione ;
formula_weight	551.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	32

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6. Citations (1)

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length_a	51.820 Å
length_b	140.910 Å
length_c	124.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.570 Å
resolution_low	48.630 Å
r_factor	0.2317
r_work	0.2291
r_free	0.2795

fit	/app/data/saxs_computation/sz/9szo/9szo.fit
pddf	/app/data/pr_computation/sz/9szo/9szo.pr.out
profile	/app/data/saxs_computation/sz/9szo/9szo.dat

Crystal structure of the catalytic domain of USP7 in complex with Compound 13

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