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9qba

Human TRIM21 PRYSPRY domain in complex with AL236

Method: X-RAY DIFFRACTION D_max: 49.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qba
deposition_date	2025-03-01
title	Human TRIM21 PRYSPRY domain in complex with AL236
keywords	TRIM21, PRYSPRY Domain, E3 ligase, Inhibitor, 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	16.24 Å
rg_electron	15.09 Å
i0	14023500.00
molecular_weight	19189.0 kDa
excluded_volume	18725 Å³
envelope_volume	27921 Å³
shell_volume	15256 Å³
envelope_diameter	50.5 Å
shell_rg	21.40 Å
envelope_rg	15.38 Å
shape_rg	15.06 Å
total_rg	15.96 Å
total_atoms	1455
n_residues	178
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	49.9 Å
rg_real	16.10 Å
rg_real_error	0.23 Å
i0_real	1.4020e+07
i0_real_error	1.6170e+05
rg_reciprocal	16.11 Å
i0_reciprocal	14020000.0000
total_estimate	0.7422
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	21.7 Å
skewness	0.083
kurtosis	-0.443
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	4342000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 0.353; Positv: 1.000; Valcen: 0.976; Smooth: 0.941

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	E3 ubiquitin-protein ligase TRIM21
formula_weight	20332.9 kDa
ec_number	2.3.2.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1584

VHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYWEVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPPCQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLCPL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	~{N}-(cyclohexylmethyl)-4-(4-fluoranyl-2-methylsulfanyl-phenyl)-2-methylsulfonyl-benzamide
formula_weight	435.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	123

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6. Citations (1)

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length_a	67.750 Å
length_b	67.750 Å
length_c	71.114 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 62
int_tables_number	171
crystal_system	—

resolution	1.450 Å
resolution_low	58.670 Å
r_factor	0.1510
r_work	0.1504
r_free	0.1620

fit	/app/data/saxs_computation/qb/9qba/9qba.fit
pddf	/app/data/pr_computation/qb/9qba/9qba.pr.out
profile	/app/data/saxs_computation/qb/9qba/9qba.dat

Human TRIM21 PRYSPRY domain in complex with AL236

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