3zix

Clostridium perfringens Enterotoxin with the N-terminal 37 residues deleted

Method: X-RAY DIFFRACTION

▼

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

HEAT-LABILE ENTEROTOXIN B CHAIN

CLOSTRIDIUM PERFRINGENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 3 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELTB_CLOPF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–286； UniProt 38–319 Author chain B； PDBConstruct 5–286； UniProt 38–319 Author chain C； PDBConstruct 5–286； UniProt 38–319 Author chain D； PDBConstruct 5–286； UniProt 38–319 Author chain E； PDBConstruct 5–286； UniProt 38–319 Author chain F； PDBConstruct 5–286； UniProt 38–319

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3zix
Deposition date deposition_date	2013-01-14
Structure title title	Clostridium perfringens Enterotoxin with the N-terminal 37 residues deleted
Keywords keywords	TOXIN, BETA PORE-FORMING-TOXIN, CYTOTOXICITY MUTANT; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3zix__assembly_1__model_1

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

Download this curve (.dat)

3zix__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zix__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.40 Å
Rg (electron density)	26.34 Å
Total Rg	26.70 Å
Atom count	2259
Residues	286
Excluded volume	40151 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zix__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zix__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3zix__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3zix__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3zix__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3zix__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HEAT-LABILE ENTEROTOXIN B CHAIN
Molecular weight formula_weight	31524.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15361

GAMGSDGLYVIDKGDGWILGEPSVVSSQILNPNETGTFSQSLTKSKEVSINVNFSVGFTSEFIQASVEYGFGITIGEQNTIERSVSTTAGPNEYVYYKVYATYRKYQAIRISHGNISDDGSIYKLTGIWLSKTSADSLGNIDQGSLIETGERCVLTVPSTDIEKEILDLAAATERLNLTDALNSNPAGNLYDWRSSNSYPWTQKLNLHLTITATGQKYRILASKIVDFNIYSNNFNNLVKLEQSLGDGVKDHYVDISLDAGQYVLVMKANSSYSGNYPYSILFQKF

Source Source

Source organism organism	CLOSTRIDIUM PERFRINGENS
NCBI taxonomy ID ncbi_taxonomy_id	1502
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1761

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d3zixa1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.8 — Aerolisin/ETX pore-forming domain
Superfamily Superfamily superfamily	f.8.1 — Aerolisin/ETX pore-forming domain
Family Family family	f.8.1.3 — Clostridium perfringens enterotoxin (CPE), pore-forming domain

Domain ID domain_id	d3zixa2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.37 — Clostridium perfringens enterotoxin (CPE), C-terminal domain

Domain ID domain_id	d3zixa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3zixb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.8 — Aerolisin/ETX pore-forming domain
Superfamily Superfamily superfamily	f.8.1 — Aerolisin/ETX pore-forming domain
Family Family family	f.8.1.3 — Clostridium perfringens enterotoxin (CPE), pore-forming domain

Domain ID domain_id	d3zixb2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.37 — Clostridium perfringens enterotoxin (CPE), C-terminal domain

Domain ID domain_id	d3zixb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3zixc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.8 — Aerolisin/ETX pore-forming domain
Superfamily Superfamily superfamily	f.8.1 — Aerolisin/ETX pore-forming domain
Family Family family	f.8.1.3 — Clostridium perfringens enterotoxin (CPE), pore-forming domain

Domain ID domain_id	d3zixc2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.37 — Clostridium perfringens enterotoxin (CPE), C-terminal domain

Domain ID domain_id	d3zixc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3zixd1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.8 — Aerolisin/ETX pore-forming domain
Superfamily Superfamily superfamily	f.8.1 — Aerolisin/ETX pore-forming domain
Family Family family	f.8.1.3 — Clostridium perfringens enterotoxin (CPE), pore-forming domain

Domain ID domain_id	d3zixd2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.37 — Clostridium perfringens enterotoxin (CPE), C-terminal domain

Domain ID domain_id	d3zixd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3zixe1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.8 — Aerolisin/ETX pore-forming domain
Superfamily Superfamily superfamily	f.8.1 — Aerolisin/ETX pore-forming domain
Family Family family	f.8.1.3 — Clostridium perfringens enterotoxin (CPE), pore-forming domain

Domain ID domain_id	d3zixe2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.37 — Clostridium perfringens enterotoxin (CPE), C-terminal domain

Domain ID domain_id	d3zixe3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3zixf1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.8 — Aerolisin/ETX pore-forming domain
Superfamily Superfamily superfamily	f.8.1 — Aerolisin/ETX pore-forming domain
Family Family family	f.8.1.3 — Clostridium perfringens enterotoxin (CPE), pore-forming domain

Domain ID domain_id	d3zixf2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.37 — Clostridium perfringens enterotoxin (CPE), C-terminal domain

Domain ID domain_id	d3zixf3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	3zixA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3zixA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1050 —

Domain ID domain_id	3zixB01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3zixB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1050 —

Domain ID domain_id	3zixC01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3zixC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1050 —

Domain ID domain_id	3zixD01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3zixD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1050 —

Domain ID domain_id	3zixE01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3zixE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1050 —

Domain ID domain_id	3zixF01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3zixF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1050 —

▶

Unit-cell length a length_a	191.680 Å
Unit-cell length b length_b	128.290 Å
Unit-cell length c length_c	137.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	133.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	47.030 Å
R factor r_factor	0.1775
R_work r_work	0.1764
R_free r_free	0.1970

Clostridium perfringens Enterotoxin with the N-terminal 37 residues deleted

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

HEAT-LABILE ENTEROTOXIN B CHAIN

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

3zix__assembly_1__model_1

3zix__assembly_1__model_1 | I(q)

3zix__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) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (2)

Clostridium perfringens Enterotoxin with the N-terminal 37 residues deleted

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

HEAT-LABILE ENTEROTOXIN B CHAIN

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

3zix__assembly_1__model_1

3zix__assembly_1__model_1 | I(q)

3zix__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) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (2)