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9ysm

Human DCTPP1 bound to MPD

Method: X-RAY DIFFRACTION D_max: 84.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ysm
deposition_date	2025-10-19
last_revision	2026-06-10
title	Human DCTPP1 bound to MPD
keywords	Inhibitor, pyrophosphatase, HYDROLASE, HYDROLASE-INHIBITOR complex; 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	27.11 Å
rg_electron	26.41 Å
i0	38067400.00
molecular_weight	49368.0 kDa
excluded_volume	62599 Å³
envelope_volume	75929 Å³
shell_volume	24629 Å³
envelope_diameter	88.4 Å
shell_rg	32.78 Å
envelope_rg	26.55 Å
shape_rg	26.46 Å
total_rg	27.02 Å
total_atoms	6999
n_residues	419
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	84.1 Å
rg_real	27.20 Å
rg_real_error	0.51 Å
i0_real	3.8070e+07
i0_real_error	5.3040e+05
rg_reciprocal	27.17 Å
i0_reciprocal	38070000.0000
total_estimate	0.8896
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.1 Å
skewness	0.372
kurtosis	-0.601
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	8189000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.882

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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	7293

GRFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKTDGEPGPQGWSPRERAALQEELSDVLIYLVALAARCRVDLPLAVLSKMDINRRRYP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	11

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	294

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6. Citations (1)

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length_a	61.907 Å
length_b	41.765 Å
length_c	94.208 Å
angle_alpha	90.00 °
angle_beta	93.89 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 2 1
int_tables_number	3
crystal_system	monoclinic

resolution	1.810 Å
resolution_low	28.770 Å
r_factor	0.1844
r_work	0.1825
r_free	0.2232

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

Human DCTPP1 bound to MPD

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