SAXSdb — 8c8i

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial ;

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Orf20 × 3 （Q9F0J8） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DUT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 112–239 Author chain B； PDBConstruct 1–128； UniProt 112–239 Author chain C； PDBConstruct 1–128； UniProt 112–239

Orf20

Staphylococcus aureus

UniProt Q9F0J8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	;Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial ; × 3 （P33316） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9F0J8_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–147； UniProt 7–153 Author chain E； PDBConstruct 1–147； UniProt 7–153 Author chain F； PDBConstruct 1–147； UniProt 7–153

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	8c8i
Deposition date deposition_date	2023-01-20
Structure title title	Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)
Keywords keywords	Inhibitor, Complex, dUTPase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8c8i__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8c8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8c8i__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.32 Å
Rg (electron density)	29.27 Å
Total Rg	29.82 Å
Atom count	6111
Residues	821
Excluded volume	107730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8c8i__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial ;
Molecular weight formula_weight	14178.1 kDa
EC 编号 ec_number	3.6.1.23
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6111

MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALDDT

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Orf20
Molecular weight formula_weight	17209.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDLYDETIKLLELLKESKINVNDIDYDYVLKLYKQILS

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

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	1

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Unit-cell length a length_a	78.450 Å
Unit-cell length b length_b	82.660 Å
Unit-cell length c length_c	139.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	52.690 Å
R factor r_factor	0.1960
R_work r_work	0.1932
R_free r_free	0.2509

Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial ;

State in the Current Structure

Other States of the Same Protein in the Database

Orf20

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8c8i__assembly_1__model_1

8c8i__assembly_1__model_1 | I(q)

8c8i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)

Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Orf20

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8c8i__assembly_1__model_1

8c8i__assembly_1__model_1 | I(q)

8c8i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)