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9ysp

Human DCTPP1 bound to a Class III inhibitor

Method: X-RAY DIFFRACTION D_max: 70.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ysp
deposition_date	2025-10-19
last_revision	2026-06-10
title	Human DCTPP1 bound to a Class III 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	23.10 Å
rg_electron	21.58 Å
i0	41260700.00
molecular_weight	50249.0 kDa
excluded_volume	63003 Å³
envelope_volume	72533 Å³
shell_volume	27064 Å³
envelope_diameter	77.5 Å
shell_rg	29.19 Å
envelope_rg	21.80 Å
shape_rg	21.48 Å
total_rg	22.76 Å
total_atoms	7012
n_residues	425
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	70.5 Å
rg_real	22.95 Å
rg_real_error	0.38 Å
i0_real	4.1260e+07
i0_real_error	4.9680e+05
rg_reciprocal	22.98 Å
i0_reciprocal	41260000.0000
total_estimate	0.6658
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.109
kurtosis	-0.511
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	7540000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 0.999; Sysdev: 0.307; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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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	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7315

GRFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKTDGEPGPQGWSPRERAALQEELSDVLIYLVALAARCRVDLPLAVLSKMDINRRRYP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	4-(4-chlorophenyl)-6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-(methylsulfanyl)pyrimidine-5-carbonitrile
formula_weight	389.9 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	303

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6. Citations (1)

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length_a	61.959 Å
length_b	80.964 Å
length_c	99.790 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	1.750 Å
resolution_low	29.310 Å
r_factor	0.1662
r_work	0.1653
r_free	0.1907

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

Human DCTPP1 bound to a Class III 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