TRIM21 PRYSPRY bound to compound 38

Method: X-RAY DIFFRACTION D_max: 80.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q9q
deposition_date	2025-02-26
title	TRIM21 PRYSPRY bound to compound 38
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	24.85 Å
rg_electron	23.98 Å
i0	29845800.00
molecular_weight	42674.0 kDa
excluded_volume	53561 Å³
envelope_volume	63833 Å³
shell_volume	22849 Å³
envelope_diameter	84.2 Å
shell_rg	30.29 Å
envelope_rg	23.94 Å
shape_rg	23.95 Å
total_rg	24.85 Å
total_atoms	5908
n_residues	366
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	80.6 Å
rg_real	24.94 Å
rg_real_error	0.63 Å
i0_real	2.9850e+07
i0_real_error	4.6370e+05
rg_reciprocal	24.92 Å
i0_reciprocal	29850000.0000
total_estimate	0.7974
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.3 Å
skewness	0.395
kurtosis	-0.505
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	10410000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.000

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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	44.905 Å
length_b	61.067 Å
length_c	67.269 Å
angle_alpha	90.00 °
angle_beta	99.15 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.253 Å
resolution_low	44.993 Å
r_factor	—
r_work	0.2516
r_free	0.3251

description	E3 ubiquitin-protein ligase TRIM21
formula_weight	22518.2 kDa
ec_number	2.3.2.27
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	B,A
atom_count	5908

TRIM21 PRYSPRY bound to compound 38

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

description	;(2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(furan-2-yl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide ;
formula_weight	495.6 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/q9/9q9q/9q9q.fit
pddf	/app/data/pr_computation/q9/9q9q/9q9q.pr.out
profile	/app/data/saxs_computation/q9/9q9q/9q9q.dat