TRIM21 PRYSPRY bound to compound 36

Method: X-RAY DIFFRACTION D_max: 110.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q9o
deposition_date	2025-02-26
title	TRIM21 PRYSPRY bound to compound 36
keywords	TRIM21, E3 ligase, PROTAC, PRYSPRY, LIGASE; LIGASE
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	33.60 Å
rg_electron	32.98 Å
i0	112480000.00
molecular_weight	85549.0 kDa
excluded_volume	107180 Å³
envelope_volume	138570 Å³
shell_volume	36052 Å³
envelope_diameter	114.4 Å
shell_rg	38.65 Å
envelope_rg	32.65 Å
shape_rg	32.97 Å
total_rg	33.48 Å
total_atoms	11804
n_residues	732
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	110.0 Å
rg_real	33.66 Å
rg_real_error	0.83 Å
i0_real	1.1250e+08
i0_real_error	1.6830e+06
rg_reciprocal	33.63 Å
i0_reciprocal	112500000.0000
total_estimate	0.8798
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	30.4 Å
skewness	0.329
kurtosis	-0.587
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	78920000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.876

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	60.685 Å
length_b	74.380 Å
length_c	90.109 Å
angle_alpha	90.00 °
angle_beta	90.10 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.462 Å
resolution_low	50.427 Å
r_factor	—
r_work	0.3017
r_free	0.3680

description	E3 ubiquitin-protein ligase TRIM21
formula_weight	22518.2 kDa
ec_number	2.3.2.27
src_method	man
entity_count	4

type	polypeptide(L)
strand_id	B,A,C,D
atom_count	11804

TRIM21 PRYSPRY bound to compound 36

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

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

description	4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide
formula_weight	520.6 kDa
src_method	syn
entity_count	4

fit	/app/data/saxs_computation/q9/9q9o/9q9o.fit
pddf	/app/data/pr_computation/q9/9q9o/9q9o.pr.out
profile	/app/data/saxs_computation/q9/9q9o/9q9o.dat