SAXSdb — 3t70

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative ;

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PEPTIDE GLY-HIS-GLY × 1 2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine × 3 SULFATE ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8II92_PLAF7
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	3t70
Deposition date deposition_date	2011-07-29
Structure title title	5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase
Keywords keywords	dUTP binding, Nucleus, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

3t70__assembly_1__model_1

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

Download this curve (.dat)

3t70__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3t70__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.37 Å
Rg (electron density)	21.96 Å
Total Rg	22.97 Å
Atom count	3578
Residues	437
Excluded volume	64246 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3t70__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	;Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative ;
Molecular weight formula_weight	20632.2 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	4081

MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGSTSNNKYEAHHHHHH

Source Source

Source organism organism	Plasmodium falciparum
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PEPTIDE GLY-HIS-GLY
Molecular weight formula_weight	270.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GHG

Entity 3 Entity 3 non-polymer

Description description	2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine
Molecular weight formula_weight	407.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	395

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3t70A01
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	3t70B01
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	3t70C01
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	76.750 Å
Unit-cell length b length_b	76.750 Å
Unit-cell length c length_c	105.830 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	1.800 Å
Low-resolution limit resolution_low	37.890 Å
R factor r_factor	0.2009
R_work r_work	0.1992
R_free r_free	0.2323

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative ;

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

3t70__assembly_1__model_1

3t70__assembly_1__model_1 | I(q)

3t70__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative ;

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

3t70__assembly_1__model_1

3t70__assembly_1__model_1 | I(q)

3t70__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)