1ogk

The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP

Method: X-RAY DIFFRACTION

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

DEOXYURIDINE TRIPHOSPHATASE

TRYPANOSOMA CRUZI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	DEOXYURIDINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	DEOXYURIDINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O15923_TRYCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 1–283 Author chain B； PDBConstruct 1–283； UniProt 1–283 Author chain D； PDBConstruct 1–283； UniProt 1–283 Author chain E； PDBConstruct 1–283； UniProt 1–283

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	1ogk
Deposition date deposition_date	2003-05-07
Structure title title	The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP
Keywords keywords	DIMER, 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.

1ogk__assembly_1__model_1

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

Download this curve (.dat)

1ogk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ogk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.63 Å
Rg (electron density)	24.57 Å
Total Rg	25.42 Å
Atom count	3838
Residues	470
Excluded volume	68492 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ogk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ogk__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ogka_
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	d1ogkb_
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	d1ogkd_
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	d1ogke_
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 (8 domains)

Domain ID domain_id	1ogkA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1680 — all-alpha NTP pyrophosphatases
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

Domain ID domain_id	1ogkE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1670 — all-alpha NTP pyrophosphatase
Homologous superfamily homologous superfamily	10 — Type II deoxyuridine triphosphatase

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Unit-cell length a length_a	106.386 Å
Unit-cell length b length_b	50.307 Å
Unit-cell length c length_c	111.387 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	111.800 Å
R factor r_factor	0.2090
R_work r_work	0.2050
R_free r_free	0.2730

Description description	DEOXYURIDINE TRIPHOSPHATASE
Molecular weight formula_weight	32104.3 kDa
EC 编号 ec_number	3.6.1.23
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	7784

The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP

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

DEOXYURIDINE TRIPHOSPHATASE

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

1ogk__assembly_1__model_1

1ogk__assembly_1__model_1 | I(q)

1ogk__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	TRYPANOSOMA CRUZI
NCBI taxonomy ID ncbi_taxonomy_id	5693
Host organism host_organism	ESCHERICHIA COLI

Description description	DEOXYURIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	388.2 kDa
Source method src_method	syn
Copy count entity_count	3

The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP

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

DEOXYURIDINE TRIPHOSPHATASE

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

1ogk__assembly_1__model_1

1ogk__assembly_1__model_1 | I(q)

1ogk__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)