SAXSdb — 9ysh

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1. Structure Basics

entry_id	9ysh
deposition_date	2025-10-18
last_revision	2026-05-20
title	Allosteric inhibitor of human DNA polymerase theta
keywords	inhibitor, complex, DNA BINDING PROTEIN, TRANSFERASE-INHIBITOR complex; DNA BINDING PROTEIN,TRANSFERASE/INHIBITOR
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	42.80 Å
rg_electron	43.03 Å
i0	746164000.00
molecular_weight	144380.0 kDa
excluded_volume	136840 Å³
envelope_volume	262020 Å³
shell_volume	52864 Å³
envelope_diameter	149.9 Å
shell_rg	45.50 Å
envelope_rg	42.47 Å
shape_rg	43.05 Å
total_rg	43.09 Å
total_atoms	10820
n_residues	1338
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	148.5 Å
rg_real	43.09 Å
rg_real_error	1.42 Å
i0_real	7.4620e+08
i0_real_error	1.4720e+07
rg_reciprocal	42.80 Å
i0_reciprocal	745900000.0000
total_estimate	0.8365
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.1 Å
skewness	0.476
kurtosis	-0.474
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	62470000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.800

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	DNA polymerase theta
formula_weight	75200.1 kDa
ec_number	2.7.7.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	10952

GASSSSESLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRSLTSSKTGFPIKGCDDTLVVGLAVCWGGRDAYYFSLQKESLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPNRELGRQFSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRDFEIKMPTLADRGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKSHGHREGMLQSDQTGGMFCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELKDFDV

Source

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

Entity 2 polymer

description	;DNA (5'-D(CPGPTPCPCPAPAPTPGPAPCPAPGPCP*C)-3') ;
formula_weight	5157.4 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	B,E

CGTCCAATGACAGCCGC

Entity 3 polymer

description	;DNA (5'-D(GPGPCPTPGPTPCPAPTPTP*G)-3') ;
formula_weight	3998.6 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,F

GCGGCTGTCATTG

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
formula_weight	491.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)pyridine-3-carboxamide
formula_weight	519.4 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	132

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6. Citations (2)

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length_a	249.130 Å
length_b	66.634 Å
length_c	151.939 Å
angle_alpha	90.00 °
angle_beta	122.73 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.710 Å
resolution_low	65.510 Å
r_factor	0.2213
r_work	0.2198
r_free	0.2513

fit	/app/data/saxs_computation/ys/9ysh/9ysh.fit
pddf	/app/data/pr_computation/ys/9ysh/9ysh.pr.out
profile	/app/data/saxs_computation/ys/9ysh/9ysh.dat

Allosteric inhibitor of human DNA polymerase theta

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)