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9s1b

WRN helicase in complex with covalent inhibitor GSK_WRN3

Method: X-RAY DIFFRACTION D_max: 85.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1b
deposition_date	2025-07-18
last_revision	2026-05-27
title	WRN helicase in complex with covalent inhibitor GSK_WRN3
keywords	Inhibitor, Covalent, Helicase, allosteric, HYDROLASE; HYDROLASE
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	24.39 Å
rg_electron	23.77 Å
i0	73283100.00
molecular_weight	44322.0 kDa
excluded_volume	42589 Å³
envelope_volume	72787 Å³
shell_volume	25889 Å³
envelope_diameter	86.8 Å
shell_rg	30.46 Å
envelope_rg	23.78 Å
shape_rg	23.77 Å
total_rg	24.34 Å
total_atoms	3337
n_residues	415
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	85.1 Å
rg_real	24.40 Å
rg_real_error	0.68 Å
i0_real	7.3280e+07
i0_real_error	1.1060e+06
rg_reciprocal	24.40 Å
i0_reciprocal	73280000.0000
total_estimate	0.8631
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	82.4 Å
skewness	0.384
kurtosis	-0.270
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	10570000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN ;
formula_weight	50635.3 kDa
ec_number	3.1.-.-,5.6.2.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3423

MGHHHHHHENLYFQGSNEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEKCCDNCRSRL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-5-oxidanyl-2-oxidanylidene-6-phenyl-1~{H}-pyridine-3-carboxamide
formula_weight	348.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	61

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6. Citations (1)

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length_a	68.850 Å
length_b	71.938 Å
length_c	121.555 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.218 Å
resolution_low	61.910 Å
r_factor	0.2484
r_work	0.2462
r_free	0.2939

fit	/app/data/saxs_computation/s1/9s1b/9s1b.fit
pddf	/app/data/pr_computation/s1/9s1b/9s1b.pr.out
profile	/app/data/saxs_computation/s1/9s1b/9s1b.dat