SAXSdb — 9yso

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1. Protein Identity and Related Structures Protein Identity & Related Structures

dCTP pyrophosphatase 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 21–130 Chain C； UniProt 21–130 Chain E； UniProt 21–130 Chain G； UniProt 21–130	Not recorded	(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 × 4 MAGNESIUM ION × 4 PROLINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.70 Å R-free 0.214
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 21–130 Chain D； UniProt 21–130 Chain F； UniProt 21–130 Chain H； UniProt 21–130	Not recorded	(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 × 4 MAGNESIUM ION × 4 PROLINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.70 Å R-free 0.214

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YSO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MU5 Human DCTPP1 bound to Triptolide Deposited 2021-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 21–130（110 aa） Chain C 21–130（110 aa） Chain E 21–130（110 aa） Chain G 21–130（110 aa）	Not recorded	MG MAGNESIUM ION × 4 TLI triptolide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Tris 7.5; 8% PEG3350; 300mM Proline	Resolution 2.20 Å R-free 0.235
7MU5 Human DCTPP1 bound to Triptolide Deposited 2021-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 21–130（110 aa） Chain D 21–130（110 aa） Chain F 21–130（110 aa） Chain H 21–130（110 aa）	Not recorded	MG MAGNESIUM ION × 2 TLI triptolide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Tris 7.5; 8% PEG3350; 300mM Proline	Resolution 2.20 Å R-free 0.235
9YSM Human DCTPP1 bound to MPD Deposited 2025-10-19	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 21–130（110 aa） Chain B 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.81 Å R-free 0.223
9YSM Human DCTPP1 bound to MPD Deposited 2025-10-19	Different construct Different mutation/modification Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 21–130（110 aa） Chain D 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.81 Å R-free 0.223
9YSN Human DCTPP1 bound to a Class I inhibitor Deposited 2025-10-19	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 21–130（110 aa） Chain B 21–130（110 aa） Chain C 21–130（110 aa） Chain F 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.228
9YSN Human DCTPP1 bound to a Class I inhibitor Deposited 2025-10-19	Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain D 21–130（110 aa） Chain E 21–130（110 aa） Chain G 21–130（110 aa） Chain H 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.228
9YSP Human DCTPP1 bound to a Class III inhibitor Deposited 2025-10-19	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 21–130（110 aa） Chain B 21–130（110 aa） Chain C 21–130（110 aa） Chain D 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.75 Å R-free 0.191

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCTP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 21–130 Author chain B； PDBConstruct 1–110； UniProt 21–130 Author chain C； PDBConstruct 1–110； UniProt 21–130 Author chain D； PDBConstruct 1–110； UniProt 21–130 Author chain E； PDBConstruct 1–110； UniProt 21–130 Author chain F； PDBConstruct 1–110； UniProt 21–130 Author chain G； PDBConstruct 1–110； UniProt 21–130 Author chain H； PDBConstruct 1–110； UniProt 21–130

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yso
Deposition date deposition_date	2025-10-19
最后修订 last_revision	2026-06-10
Structure title title	Human DCTPP1 bound to a Class II inhibitor
Keywords keywords	Inhibitor, pyrophosphatase, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.77 Å
Radius of gyration Rg (electron density) rg_electron	29.64 Å
Forward intensity I(0) i0	160754000.00
Molecular weight molecular_weight	101330.0 kDa
Excluded volume excluded_volume	126970 Å³
Envelope volume envelope_volume	153430 Å³
Hydration-shell volume shell_volume	42238 Å³
Envelope diameter envelope_diameter	100.0 Å
Shell Rg shell_rg	37.80 Å
Envelope Rg envelope_rg	29.51 Å
Shape Rg shape_rg	29.56 Å
Total Rg total_rg	30.57 Å
Total atoms total_atoms	14208
Residues n_residues	853
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.8 Å
Rg (real space) rg_real	30.68 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.6080e+08
I(0) uncertainty (real space) i0_real_error	2.5380e+06
Rg (reciprocal space) rg_reciprocal	30.72 Å
I(0) (reciprocal space) i0_reciprocal	160800000.0000
Solution quality estimate total_estimate	0.8975
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.4 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.435
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41630000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	dCTP pyrophosphatase 1
Molecular weight formula_weight	12686.4 kDa
EC 编号 ec_number	3.6.1.12
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	14933

GRFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKTDGEPGPQGWSPRERAALQEELSDVLIYLVALAARCRVDLPLAVLSKMDINRRRYP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description 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
Molecular weight formula_weight	397.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	PROLINE
Molecular weight formula_weight	115.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	725

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8. Citations (1)

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Unit-cell length a length_a	60.553 Å
Unit-cell length b length_b	61.021 Å
Unit-cell length c length_c	73.919 Å
Unit-cell angle α angle_alpha	71.21 °
Unit-cell angle β angle_beta	75.06 °
Unit-cell angle γ angle_gamma	71.85 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	28.680 Å
R factor r_factor	0.1753
R_work r_work	0.1745
R_free 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

Human DCTPP1 bound to a Class II inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

dCTP pyrophosphatase 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction