SAXSdb — 6sqy

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

dCTP pyrophosphatase 1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCTP1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–170； UniProt 1–170 Author chain D； PDBConstruct 1–170； UniProt 1–170

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	6sqy
Deposition date deposition_date	2019-09-04
Structure title title	Mouse dCTPase in complex with dCMP
Keywords keywords	dCMP complex, 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.

6sqy__assembly_1__model_1

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

Download this curve (.dat)

6sqy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6sqy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.43 Å
Rg (electron density)	22.13 Å
Total Rg	23.04 Å
Atom count	3768
Residues	454
Excluded volume	66594 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6sqy__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 (4)

Entity 1 Entity 1 polymer

Description description	dCTP pyrophosphatase 1
Molecular weight formula_weight	18790.9 kDa
EC 编号 ec_number	3.6.1.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	2108

MSTAGDGERGTVGQEDSAAAMPFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKMDTNRQRYPVHLSRGSACKYTDLPRGTISENQAVGAGDPASELRDQAST

Source Source

Source organism organism	Mus musculus
Common name common_name	House mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	307.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6sqya_
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.204.1.2 — MazG-like

Domain ID domain_id	d6sqyd_
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.204.1.2 — MazG-like

CATH v4.4 (2 domains)

Domain ID domain_id	6sqyA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1080 — MazG-like

Domain ID domain_id	6sqyD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1080 — MazG-like

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Unit-cell length a length_a	59.277 Å
Unit-cell length b length_b	59.277 Å
Unit-cell length c length_c	140.537 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	54.620 Å
R factor r_factor	0.1807
R_work r_work	0.1788
R_free r_free	0.2145

Mouse dCTPase in complex with dCMP

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

dCTP pyrophosphatase 1

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

6sqy__assembly_1__model_1

6sqy__assembly_1__model_1 | I(q)

6sqy__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)

Mouse dCTPase in complex with dCMP

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

dCTP pyrophosphatase 1

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

6sqy__assembly_1__model_1

6sqy__assembly_1__model_1 | I(q)

6sqy__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)