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9q9r

TRIM21 PRYSPRY bound to compound 209

Method: X-RAY DIFFRACTION D_max: 51.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q9r
deposition_date	2025-02-26
title	TRIM21 PRYSPRY bound to compound 209
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	16.89 Å
rg_electron	15.38 Å
i0	8203130.00
molecular_weight	21451.0 kDa
excluded_volume	26949 Å³
envelope_volume	29812 Å³
shell_volume	15904 Å³
envelope_diameter	50.3 Å
shell_rg	21.80 Å
envelope_rg	15.67 Å
shape_rg	15.35 Å
total_rg	16.61 Å
total_atoms	2972
n_residues	183
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	51.6 Å
rg_real	16.74 Å
rg_real_error	0.20 Å
i0_real	8.2030e+06
i0_real_error	9.1460e+04
rg_reciprocal	16.76 Å
i0_reciprocal	8203000.0000
total_estimate	0.8917
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.8 Å
skewness	0.033
kurtosis	-0.440
angular_range	— – 0.4700 Å⁻¹
current_alpha	0.0000
highest_alpha	2892000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	E3 ubiquitin-protein ligase TRIM21
formula_weight	22518.2 kDa
ec_number	2.3.2.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	2983

MAHHHHHHMVHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYWEVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPPCQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLCPLNIGSQGSTDY

Source

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

Entity 2 non-polymer

description	;(2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-[2-[2-(2-hydroxyethyloxy)ethoxy]phenyl]propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide ;
formula_weight	609.8 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	11

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6. Citations (1)

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length_a	37.068 Å
length_b	60.827 Å
length_c	42.223 Å
angle_alpha	90.00 °
angle_beta	112.54 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.331 Å
resolution_low	30.432 Å
r_factor	—
r_work	0.2224
r_free	0.3137

fit	/app/data/saxs_computation/q9/9q9r/9q9r.fit
pddf	/app/data/pr_computation/q9/9q9r/9q9r.pr.out
profile	/app/data/saxs_computation/q9/9q9r/9q9r.dat

TRIM21 PRYSPRY bound to compound 209

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