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9rur

Structure of WRN in complex with ATPgS and covalent ligand Compound 4d

Method: X-RAY DIFFRACTION D_max: 108.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rur
deposition_date	2025-07-04
title	Structure of WRN in complex with ATPgS and covalent ligand Compound 4d
keywords	DNA Damage Repair, Inhibitor, Complex, Helicase, 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	32.41 Å
rg_electron	32.15 Å
i0	137735000.00
molecular_weight	92429.0 kDa
excluded_volume	115360 Å³
envelope_volume	147800 Å³
shell_volume	38903 Å³
envelope_diameter	107.8 Å
shell_rg	38.58 Å
envelope_rg	31.83 Å
shape_rg	32.15 Å
total_rg	32.64 Å
total_atoms	6438
n_residues	796
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	108.6 Å
rg_real	32.51 Å
rg_real_error	0.76 Å
i0_real	1.3770e+08
i0_real_error	2.0120e+06
rg_reciprocal	32.47 Å
i0_reciprocal	137700000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.401
kurtosis	-0.414
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	38660000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	;Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN ;
formula_weight	48597.1 kDa
ec_number	3.1.-.-,5.6.2.4
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6715

GMNEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEKCCDNCRS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	2-ethylsulfanyl-~{N}-[1-[(4-fluorophenyl)methyl]indazol-3-yl]ethanamide
formula_weight	343.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	182

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6. Citations (1)

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length_a	89.980 Å
length_b	89.980 Å
length_c	241.352 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	2.296 Å
resolution_low	84.310 Å
r_factor	0.2519
r_work	0.2504
r_free	0.2806

fit	/app/data/saxs_computation/ru/9rur/9rur.fit
pddf	/app/data/pr_computation/ru/9rur/9rur.pr.out
profile	/app/data/saxs_computation/ru/9rur/9rur.dat