Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)

entry_id	12zj
deposition_date	2026-04-24
last_revision	2026-06-10
title	Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
keywords	Deubiquitinase TRAF domain Complex Ubiquitin signaling, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	29.84 Å
rg_electron	29.60 Å
i0	48364800.00
molecular_weight	53593.0 kDa
excluded_volume	66541 ų
envelope_volume	87744 ų
shell_volume	26966 ų
envelope_diameter	105.5 Å
shell_rg	33.99 Å
envelope_rg	29.58 Å
shape_rg	29.60 Å
total_rg	30.05 Å
total_atoms	3791
n_residues	458
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	102.8 Å
rg_real	30.12 Å
rg_real_error	1.08 Å
i0_real	4.8360e+07
i0_real_error	8.2120e+05
rg_reciprocal	30.00 Å
i0_reciprocal	48360000.0000
total_estimate	0.8365
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.1 Å
skewness	0.568
kurtosis	-0.242
angular_range	— – 0.2650 Å−1
current_alpha	0.0000
highest_alpha	6004000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.773; Smooth: 0.876

Unit Cell

length_a	57.483 Å
length_b	50.696 Å
length_c	82.974 Å
angle_alpha	90.00 °
angle_beta	103.78 °
angle_gamma	90.00 °
z_pdb	6

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

Refinement

resolution	1.630 Å
resolution_low	41.500 Å
r_factor	0.1950
r_work	0.1940
r_free	0.2170

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/2z/12zj/pr_distribution.json
• pr_output /app/data/pr_computation/2z/12zj/12zj.pr.out
• pr_plot /app/data/visualization/pr_computation/2z/12zj/12zj_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/2z/12zj/12zj.dat
• saxs_fit /app/data/saxs_computation/2z/12zj/12zj.fit
• saxs_log /app/data/saxs_computation/2z/12zj/12zj.log
• saxs_plot /app/data/visualization/saxs_computation/2z/12zj/12zj_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/2z/12zj/12zj.fit
pddf	/app/data/pr_computation/2z/12zj/12zj.pr.out
profile	/app/data/saxs_computation/2z/12zj/12zj.dat