SAXSdb — 1w2y

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE ;

CAMPYLOBACTER JEJUNI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE ; × 2 MAGNESIUM ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9PMK9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 1–229 Author chain B； PDBConstruct 1–229； UniProt 1–229

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	1w2y
Deposition date deposition_date	2004-07-09
Structure title title	The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue dUpNHp
Keywords keywords	DUTP PYROPHOSPHATASE, DIMERIC, LIGAND COMPLEX, MAGNESIUM IONS, PATHOGEN, DRUG TARGET, 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.

1w2y__assembly_1__model_1

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

Download this curve (.dat)

1w2y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w2y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.51 Å
Rg (electron density)	22.69 Å
Total Rg	23.61 Å
Atom count	3653
Residues	435
Excluded volume	65383 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w2y__assembly_1__model_1`	dimeric （2）	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 NUCLEOTIDE HYDROLASE ;
Molecular weight formula_weight	27051.7 kDa
EC 编号 ec_number	3.6.1.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4067

MTNIEILENMLKLQQKLNDETNGLNWENGYTKEGKLISWRRCIYMECAELIDSFTWKHWKNISSLTNWENVRIEIVDIWHFILSLLLEEYRDKNNKDFKAIATEVNAVSVFQDFCKEEEYPNEGDIYGILNDIELIIHKCSGFGFNLGELLSTYFTLAIKCGLNLEILYKTYIGKNVLNIFRQNNGYKDGSYKKTWNGKEDNEVLAQILEQELDFDTIYKKLEECYKKA

Source Source

Source organism organism	CAMPYLOBACTER JEJUNI
NCBI taxonomy ID ncbi_taxonomy_id	197
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE ;
Molecular weight formula_weight	387.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	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	383

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1w2ya_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.1 — Type II deoxyuridine triphosphatase

Domain ID domain_id	d1w2yb_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.1 — Type II deoxyuridine triphosphatase

CATH v4.4 (2 domains)

Domain ID domain_id	1w2yA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4010 — all-alpha NTP pyrophosphatase fold
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1w2yB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4010 — all-alpha NTP pyrophosphatase fold
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

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Unit-cell length a length_a	66.963 Å
Unit-cell length b length_b	70.629 Å
Unit-cell length c length_c	92.850 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	8

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	55.900 Å
R factor r_factor	0.1530
R_work r_work	0.1510
R_free r_free	0.1940

The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue dUpNHp

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE ;

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

1w2y__assembly_1__model_1

1w2y__assembly_1__model_1 | I(q)

1w2y__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 (1)

The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue dUpNHp

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE ;

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

1w2y__assembly_1__model_1

1w2y__assembly_1__model_1 | I(q)

1w2y__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 (1)