SAXSdb — 3q8x

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

Antidote of epsilon-zeta postsegregational killing system

Streptococcus pyogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Zeta-toxin × 2 （Q54944） SULFATE ION × 2 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6UZC8_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–90； UniProt 1–90 Author chain C； PDBConstruct 1–90； UniProt 1–90

Zeta-toxin

Streptococcus pyogenes

UniProt Q54944

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Antidote of epsilon-zeta postsegregational killing system × 2 （Q6UZC8） SULFATE ION × 2 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZTOX_STRPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–287； UniProt 1–287 Author chain D； PDBConstruct 1–287； UniProt 1–287

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	3q8x
Deposition date deposition_date	2011-01-07
Structure title title	Structure of a toxin-antitoxin system bound to its substrate
Keywords keywords	Polynucleotide kinase fold, epsilon: antidote zeta: bacterial toxin, TRANSFERASE; TRANSFERASE
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.

3q8x__assembly_1__model_1

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

Download this curve (.dat)

3q8x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3q8x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.40 Å
Rg (electron density)	31.16 Å
Total Rg	31.78 Å
Atom count	5816
Residues	713
Excluded volume	103570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3q8x__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	Antidote of epsilon-zeta postsegregational killing system
Molecular weight formula_weight	10734.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5816

MAVTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVNLLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNKEKVA

Source Source

Source organism organism	Streptococcus pyogenes
NCBI taxonomy ID ncbi_taxonomy_id	1314
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Zeta-toxin
Molecular weight formula_weight	32445.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MANIVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQETPEFKAIQQKLESLQPPTPPIPKTPKLPGI

Source Source

Source organism organism	Streptococcus pyogenes
NCBI taxonomy ID ncbi_taxonomy_id	1314
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Molecular weight formula_weight	607.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3q8xa_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.2 — Plasmid maintenance system epsilon/zeta, antidote epsilon subunit
Family Family family	a.8.2.1 — Plasmid maintenance system epsilon/zeta, antidote epsilon subunit

Domain ID domain_id	d3q8xb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.21 — Plasmid maintenance system epsilon/zeta, toxin zeta subunit

Domain ID domain_id	d3q8xc_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.2 — Plasmid maintenance system epsilon/zeta, antidote epsilon subunit
Family Family family	a.8.2.1 — Plasmid maintenance system epsilon/zeta, antidote epsilon subunit

Domain ID domain_id	d3q8xd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.21 — Plasmid maintenance system epsilon/zeta, toxin zeta subunit

CATH v4.4 (4 domains)

Domain ID domain_id	3q8xA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3q8xB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3q8xC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3q8xD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	59.800 Å
Unit-cell length b length_b	79.990 Å
Unit-cell length c length_c	195.170 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	2.700 Å
Low-resolution limit resolution_low	46.520 Å
R factor r_factor	0.2124
R_work r_work	0.2097
R_free r_free	0.2631

Structure of a toxin-antitoxin system bound to its substrate

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

Antidote of epsilon-zeta postsegregational killing system

State in the Current Structure

Other States of the Same Protein in the Database

Zeta-toxin

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

3q8x__assembly_1__model_1

3q8x__assembly_1__model_1 | I(q)

3q8x__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of a toxin-antitoxin system bound to its substrate

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

Antidote of epsilon-zeta postsegregational killing system

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Zeta-toxin

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

3q8x__assembly_1__model_1

3q8x__assembly_1__model_1 | I(q)

3q8x__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)