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9ysn

Human DCTPP1 bound to a Class I inhibitor

Method: X-RAY DIFFRACTION D_max: 105.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ysn
deposition_date	2025-10-19
last_revision	2026-06-10
title	Human DCTPP1 bound to a Class I 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	32.89 Å
rg_electron	32.06 Å
i0	153947000.00
molecular_weight	99999.0 kDa
excluded_volume	125470 Å³
envelope_volume	158000 Å³
shell_volume	41504 Å³
envelope_diameter	112.4 Å
shell_rg	38.58 Å
envelope_rg	31.99 Å
shape_rg	31.99 Å
total_rg	32.84 Å
total_atoms	13987
n_residues	849
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	105.1 Å
rg_real	32.82 Å
rg_real_error	0.71 Å
i0_real	1.5390e+08
i0_real_error	2.5560e+06
rg_reciprocal	32.86 Å
i0_reciprocal	154000000.0000
total_estimate	0.9025
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.2 Å
skewness	0.249
kurtosis	-0.544
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	38850000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.927

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	14097

GRFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKTDGEPGPQGWSPRERAALQEELSDVLIYLVALAARCRVDLPLAVLSKMDINRRRYP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-{[7-(4-cyclohexylpiperazin-1-yl)-4-nitro-2,1,3-benzoxadiazol-5-yl]amino}ethan-1-ol
formula_weight	390.4 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	110

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6. Citations (1)

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length_a	61.637 Å
length_b	63.727 Å
length_c	67.627 Å
angle_alpha	78.44 °
angle_beta	78.10 °
angle_gamma	64.71 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.300 Å
resolution_low	26.660 Å
r_factor	0.2116
r_work	0.2109
r_free	0.2277

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

Human DCTPP1 bound to a Class I inhibitor

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