3ehw

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

Method: X-RAY DIFFRACTION

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

dUTP pyrophosphatase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 4 ;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 4 ;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6FHN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 1–164 Author chain B； PDBConstruct 1–164； UniProt 1–164 Author chain C； PDBConstruct 1–164； UniProt 1–164 Author chain X； PDBConstruct 1–164； UniProt 1–164 Author chain Y； PDBConstruct 1–164； UniProt 1–164 Author chain Z； PDBConstruct 1–164； UniProt 1–164

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	3ehw
Deposition date deposition_date	2008-09-15
Structure title title	Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site
Keywords keywords	jelly-roll, full-length C-terminal arm, enzyme-ligand complex, 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.

3ehw__assembly_1__model_1

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

Download this curve (.dat)

3ehw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ehw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.03 Å
Rg (electron density)	19.95 Å
Total Rg	20.78 Å
Atom count	3267
Residues	421
Excluded volume	57576 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ehw__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ehw__assembly_2__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	dUTP pyrophosphatase
Molecular weight formula_weight	17771.1 kDa
EC 编号 ec_number	3.6.1.23
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,X,Y,Z
Atom count atom_count	7277

MPCSEETPAISPSKRARPAEVGGMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALDDTERGSGGFGSTGKN

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 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ;
Molecular weight formula_weight	467.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	731

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3ehwa_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d3ehwb_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d3ehwc_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d3ehwx_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d3ehwy_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d3ehwz_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3ehwA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	3ehwB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	3ehwC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	3ehwX00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	3ehwY00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	3ehwZ00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

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Unit-cell length a length_a	65.446 Å
Unit-cell length b length_b	87.160 Å
Unit-cell length c length_c	70.608 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1597
R_work r_work	0.1576
R_free r_free	0.1990

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

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

dUTP pyrophosphatase

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

3ehw__assembly_1__model_1

3ehw__assembly_1__model_1 | I(q)

3ehw__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (3)

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

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

dUTP pyrophosphatase

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

3ehw__assembly_1__model_1

3ehw__assembly_1__model_1 | I(q)

3ehw__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (3)