SAXSdb — 2we1

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE ;

HUMAN HERPESVIRUS 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 1 SULFATE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DUT_EBVB9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–286； UniProt 1–278

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	2we1
Deposition date deposition_date	2009-03-27
Structure title title	EBV dUTPase mutant Asp131Asn with bound dUMP
Keywords keywords	PYROPHOSPHATASE, EPSTEIN-BARR VIRUS, NUCLEOTIDE METABOLISM, DUTPASE, MONOMER, HYDROLASE, HERPES VIRUS; 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.

2we1__assembly_1__model_1

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

Download this curve (.dat)

2we1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2we1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.93 Å
Rg (electron density)	17.87 Å
Total Rg	18.83 Å
Atom count	1971
Residues	245
Excluded volume	35130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2we1__assembly_1__model_1`	monomeric （1）	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	;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE ;
Molecular weight formula_weight	31664.3 kDa
EC 编号 ec_number	3.6.1.23
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2223

GAMGSGIPMEACPHIRYAFQNDKLLLQQASVGRLTLVNKTTILLRPMKTTTVDLGLYARPPEGHGLMLWGSTSRPVTSHVGIIDPGYTGELRLILQNQRRYNSTLRPSELKIHLAAFRYATPQMEEDKGPINHPQYPGNVGLDVSLPKDLALFPHQTVSVTLTVPPPSIPHHRPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVYLHKHHLTSFYSPHSDAGVLGPRSLFRWASCTFEEVPSLAMGDSGLSEALEGRQGRGFGSSGQ

Source Source

Source organism organism	HUMAN HERPESVIRUS 4
Common name common_name	EPSTEIN-BARR VIRUS
NCBI taxonomy ID ncbi_taxonomy_id	10377
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	308.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2we1a1
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.85.4.1 — dUTPase-like

Domain ID domain_id	d2we1a2
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.85.4.1 — dUTPase-like

CATH v4.4 (2 domains)

Domain ID domain_id	2we1A01
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	2we1A02
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	55.624 Å
Unit-cell length b length_b	56.859 Å
Unit-cell length c length_c	81.073 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	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	46.570 Å
R factor r_factor	0.1982
R_work r_work	0.1956
R_free r_free	0.2474

EBV dUTPase mutant Asp131Asn with bound dUMP

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE ;

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

2we1__assembly_1__model_1

2we1__assembly_1__model_1 | I(q)

2we1__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

EBV dUTPase mutant Asp131Asn with bound dUMP

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE ;

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

2we1__assembly_1__model_1

2we1__assembly_1__model_1 | I(q)

2we1__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)