SAXSdb — 1xdt

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

DIPHTHERIA TOXIN

Corynebacterium diphtheriae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	HEPARIN-BINDING EPIDERMAL GROWTH FACTOR × 2 （Q99075） water × 4	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 T； PDBConstruct 1–535； UniProt 33–567

HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

Homo sapiens

UniProt Q99075

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DIPHTHERIA TOXIN × 2 （P00588） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HBEGF_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 5–79； UniProt 73–147

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	1xdt
Deposition date deposition_date	1997-11-18
Structure title title	COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
Keywords keywords	;COMPLEX (TOXIN-GROWTH FACTOR), DIPHTHERIA TOXIN, RECEPTOR, HEPARIN-BINDING EPIDERMAL GROWTH FACTOR, EPIDERMAL GROWTH FACTOR, COMPLEX (TOXIN-GROWTH FACTOR) complex ;; COMPLEX (TOXIN/GROWTH FACTOR)
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.

1xdt__assembly_1__model_1

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

Download this curve (.dat)

1xdt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xdt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.11 Å
Rg (electron density)	32.28 Å
Total Rg	32.93 Å
Atom count	8612
Residues	1118
Excluded volume	152570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xdt__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 (3)

Entity 1 Entity 1 polymer

Description description	DIPHTHERIA TOXIN
Molecular weight formula_weight	58411.4 kDa
EC 编号 ec_number	2.4.2.36
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T
Atom count atom_count	4354

GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS

Source Source

Source organism organism	Corynebacterium diphtheriae
NCBI taxonomy ID ncbi_taxonomy_id	1717
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
Molecular weight formula_weight	8927.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

GSHMRVTLSSKPQALATPNKEEHGKRKKKGKGLGKKRDPCLRKYKDFCIHGECKYVKELRAPSCICHPGYHGERCHGLS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1xdtr_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d1xdtt1
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	d1xdtt2
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	d1xdtt3
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 (4 domains)

Domain ID domain_id	1xdtR00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1xdtT01
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	1xdtT02
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	1xdtT03
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	89.400 Å
Unit-cell length b length_b	103.700 Å
Unit-cell length c length_c	127.700 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1720
R_work r_work	0.1720
R_free r_free	0.2900

COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

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

DIPHTHERIA TOXIN

State in the Current Structure

Other States of the Same Protein in the Database

HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

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

1xdt__assembly_1__model_1

1xdt__assembly_1__model_1 | I(q)

1xdt__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

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

DIPHTHERIA 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

HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

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

1xdt__assembly_1__model_1

1xdt__assembly_1__model_1 | I(q)

1xdt__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)