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9yso

Human DCTPP1 bound to a Class II inhibitor

Method: X-RAY DIFFRACTION D_max: 97.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yso
deposition_date	2025-10-19
last_revision	2026-06-10
title	Human DCTPP1 bound to a Class II inhibitor
keywords	Inhibitor, pyrophosphatase, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/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	30.77 Å
rg_electron	29.64 Å
i0	160754000.00
molecular_weight	101330.0 kDa
excluded_volume	126970 Å³
envelope_volume	153430 Å³
shell_volume	42238 Å³
envelope_diameter	100.0 Å
shell_rg	37.80 Å
envelope_rg	29.51 Å
shape_rg	29.56 Å
total_rg	30.57 Å
total_atoms	14208
n_residues	853
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	97.8 Å
rg_real	30.68 Å
rg_real_error	0.75 Å
i0_real	1.6080e+08
i0_real_error	2.5380e+06
rg_reciprocal	30.72 Å
i0_reciprocal	160800000.0000
total_estimate	0.8975
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.4 Å
skewness	0.267
kurtosis	-0.435
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	41630000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	dCTP pyrophosphatase 1
formula_weight	12686.4 kDa
ec_number	3.6.1.12
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	14933

GRFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKTDGEPGPQGWSPRERAALQEELSDVLIYLVALAARCRVDLPLAVLSKMDINRRRYP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(6-methoxypyridin-3-yl)[(3S)-3-{4-[3-(propan-2-yl)-1,2,4-oxadiazol-5-yl]-1H-1,2,3-triazol-1-yl}piperidin-1-yl]methanone
formula_weight	397.4 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	PROLINE
formula_weight	115.1 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	725

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6. Citations (1)

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length_a	60.553 Å
length_b	61.021 Å
length_c	73.919 Å
angle_alpha	71.21 °
angle_beta	75.06 °
angle_gamma	71.85 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.700 Å
resolution_low	28.680 Å
r_factor	0.1753
r_work	0.1745
r_free	0.2143

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