SAXSdb — 1vyq

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

;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE ;

PLASMODIUM FALCIPARUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8II92
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 1–173 Author chain B； PDBConstruct 1–173； UniProt 1–173 Author chain C； PDBConstruct 1–173； UniProt 1–173

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	1vyq
Deposition date deposition_date	2004-05-05
Structure title title	Novel inhibitors of Plasmodium Falciparum dUTPase provide a platform for anti-malarial drug design
Keywords keywords	DRUG DESIGN, PLASMODIUM FALCIPARUM, DUTPASE, DEOXYURIDINE NUCLEOTIDOHYDROLASE, MALARIA, 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.

1vyq__assembly_1__model_1

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

Download this curve (.dat)

1vyq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vyq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.30 Å
Rg (electron density)	20.88 Å
Total Rg	21.92 Å
Atom count	3207
Residues	422
Excluded volume	57527 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vyq__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	;DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE ;
Molecular weight formula_weight	19603.2 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	3330

MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGSTSNNKY

Source Source

Source organism organism	PLASMODIUM FALCIPARUM
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE
Molecular weight formula_weight	472.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1vyqa1
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	d1vyqb_
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	d1vyqc_
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 (3 domains)

Domain ID domain_id	1vyqA01
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	1vyqB01
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	1vyqC01
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	62.830 Å
Unit-cell length b length_b	62.830 Å
Unit-cell length c length_c	121.527 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1960
R_work r_work	0.1910
R_free r_free	0.2950

Novel inhibitors of Plasmodium Falciparum dUTPase provide a platform for anti-malarial drug design

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

1vyq__assembly_1__model_1

1vyq__assembly_1__model_1 | I(q)

1vyq__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Novel inhibitors of Plasmodium Falciparum dUTPase provide a platform for anti-malarial drug design

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

1vyq__assembly_1__model_1

1vyq__assembly_1__model_1 | I(q)

1vyq__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)