SAXSdb — 7skk

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

Pertussis toxin subunit 1

Bordetella pertussis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NICOTINAMIDE × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NICOTINAMIDE × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	NICOTINAMIDE × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	NICOTINAMIDE × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOX1_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–184； UniProt 36–216 Author chain B； PDBConstruct 4–184； UniProt 36–216 Author chain C； PDBConstruct 4–184； UniProt 36–216 Author chain D； PDBConstruct 4–184； UniProt 36–216

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	7skk
Deposition date deposition_date	2021-10-21
Structure title title	pertussis toxin in complex with ADPR and Nicotinamide
Keywords keywords	TOXIN, ADP-RIBOSYLTRANSFERASE, TRANSFERASE, WHOOPING COUGH, INHIBITOR, PERTUSSIS, TRANSFERASE-INHIBITOR complex; TOXIN, TRANSFERASE/INHIBITOR
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.

7skk__assembly_1__model_1

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

Download this curve (.dat)

7skk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7skk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.79 Å
Rg (electron density)	16.84 Å
Total Rg	17.75 Å
Atom count	1477
Residues	180
Excluded volume	25283 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7skk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7skk__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7skk__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7skk__assembly_4__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Pertussis toxin subunit 1
Molecular weight formula_weight	20725.4 kDa
EC 编号 ec_number	2.4.2.-, 2.4.2.30
Mutation mutation	C41S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6673

GPGDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSSQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRR

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	737

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7skkA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	7skkB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	7skkC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	7skkD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

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Unit-cell length a length_a	34.540 Å
Unit-cell length b length_b	68.140 Å
Unit-cell length c length_c	71.730 Å
Unit-cell angle α angle_alpha	91.10 °
Unit-cell angle β angle_beta	90.20 °
Unit-cell angle γ angle_gamma	91.28 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	31.480 Å
R factor r_factor	0.1660
R_work r_work	0.1643
R_free r_free	0.1979

pertussis toxin in complex with ADPR and Nicotinamide

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

Pertussis toxin subunit 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

7skk__assembly_1__model_1

7skk__assembly_1__model_1 | I(q)

7skk__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

pertussis toxin in complex with ADPR and Nicotinamide

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

Pertussis toxin subunit 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

7skk__assembly_1__model_1

7skk__assembly_1__model_1 | I(q)

7skk__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)