1tox

DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD

Method: X-RAY DIFFRACTION

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

DIPHTHERIA TOXIN (DIMERIC)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DTX_CORBE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–535； UniProt 26–560 Author chain B； PDBConstruct 1–535； UniProt 26–560

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	1tox
Deposition date deposition_date	1995-10-06
Structure title title	DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD
Keywords keywords	TOXIN, ADP-RIBOSYLATION, GLUCOSYLTRANSFERASE, TRANSFERASE, NAD; TOXIN
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.

1tox__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1tox__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tox__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	33.55 Å
Rg (electron density)	32.78 Å
Total Rg	33.37 Å
Atom count	7978
Residues	1026
Excluded volume	141220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tox__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tox__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tox__assembly_3__model_1`	dimeric （2）	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	DIPHTHERIA TOXIN (DIMERIC)
Molecular weight formula_weight	58411.4 kDa
EC 编号 ec_number	2.4.2.36
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8295

GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1toxa1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.1 — Diphtheria toxin, C-terminal domain
Family Family family	b.2.1.1 — Diphtheria toxin, C-terminal domain

Domain ID domain_id	d1toxa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1toxa3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.2 — Diphtheria toxin, middle domain
Family Family family	f.1.2.1 — Diphtheria toxin, middle domain

Domain ID domain_id	d1toxb1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.1 — Diphtheria toxin, C-terminal domain
Family Family family	b.2.1.1 — Diphtheria toxin, C-terminal domain

Domain ID domain_id	d1toxb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1toxb3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.2 — Diphtheria toxin, middle domain
Family Family family	f.1.2.1 — Diphtheria toxin, middle domain

CATH v4.4 (6 domains)

Domain ID domain_id	1toxA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	175 — Diphtheria Toxin; domain 1
Homologous superfamily homologous superfamily	10 — Diphtheria Toxin, domain 1

Domain ID domain_id	1toxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	40 — Diphtheria toxin, translocation domain

Domain ID domain_id	1toxA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	700 — Diphtheria toxin, receptor-binding domain

Domain ID domain_id	1toxB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	175 — Diphtheria Toxin; domain 1
Homologous superfamily homologous superfamily	10 — Diphtheria Toxin, domain 1

Domain ID domain_id	1toxB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	40 — Diphtheria toxin, translocation domain

Domain ID domain_id	1toxB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	700 — Diphtheria toxin, receptor-binding domain

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Unit-cell length a length_a	105.000 Å
Unit-cell length b length_b	89.500 Å
Unit-cell length c length_c	130.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.3070

DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD

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

DIPHTHERIA TOXIN (DIMERIC)

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

1tox__assembly_3__model_1

1tox__assembly_3__model_1 | I(q)

1tox__assembly_3__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (5)

DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD

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

DIPHTHERIA TOXIN (DIMERIC)

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

1tox__assembly_3__model_1

1tox__assembly_3__model_1 | I(q)

1tox__assembly_3__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (5)