SAXSdb — 9ysm

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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 B； UniProt 21–130	Not recorded	(4S)-2-METHYL-2,4-PENTANEDIOL × 12 MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.81 Å R-free 0.223
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 21–130 Chain D； UniProt 21–130	Not recorded	(4S)-2-METHYL-2,4-PENTANEDIOL × 10 MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.81 Å R-free 0.223

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 9YSM	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 construct Different mutation/modification 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 construct Different mutation/modification 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
9YSN Human DCTPP1 bound to a Class I inhibitor 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） 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 construct Different mutation/modification 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
9YSO Human DCTPP1 bound to a Class II inhibitor 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 C 21–130（110 aa） Chain E 21–130（110 aa） Chain G 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.214
9YSO Human DCTPP1 bound to a Class II inhibitor Deposited 2025-10-19	Different construct Different mutation/modification 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	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.214
9YSP Human DCTPP1 bound to a Class III inhibitor 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） 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

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	9ysm
Deposition date deposition_date	2025-10-19
最后修订 last_revision	2026-06-10
Structure title title	Human DCTPP1 bound to MPD
Keywords keywords	Inhibitor, pyrophosphatase, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE
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	27.11 Å
Radius of gyration Rg (electron density) rg_electron	26.41 Å
Forward intensity I(0) i0	38067400.00
Molecular weight molecular_weight	49368.0 kDa
Excluded volume excluded_volume	62599 Å³
Envelope volume envelope_volume	75929 Å³
Hydration-shell volume shell_volume	24629 Å³
Envelope diameter envelope_diameter	88.4 Å
Shell Rg shell_rg	32.78 Å
Envelope Rg envelope_rg	26.55 Å
Shape Rg shape_rg	26.46 Å
Total Rg total_rg	27.02 Å
Total atoms total_atoms	6999
Residues n_residues	419
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	84.1 Å
Rg (real space) rg_real	27.20 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	3.8070e+07
I(0) uncertainty (real space) i0_real_error	5.3040e+05
Rg (reciprocal space) rg_reciprocal	27.17 Å
I(0) (reciprocal space) i0_reciprocal	38070000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.372
Kurtosis Kurtosis kurtosis	-0.601
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8189000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7293

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	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	11

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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	294

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8. Citations (1)

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Unit-cell length a length_a	61.907 Å
Unit-cell length b length_b	41.765 Å
Unit-cell length c length_c	94.208 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	monoclinic

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	28.770 Å
R factor r_factor	0.1844
R_work r_work	0.1825
R_free 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

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