SAXSdb — 7sky

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 36–216	Not recorded	IOD IODIDE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；25% PEG 3350, 0.2M KI	Resolution 1.37 Å R-free 0.224
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 36–216	Not recorded	IOD IODIDE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；25% PEG 3350, 0.2M KI	Resolution 1.37 Å R-free 0.224
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 36–216	Not recorded	IOD IODIDE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；25% PEG 3350, 0.2M KI	Resolution 1.37 Å R-free 0.224
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 36–216	Not recorded	IOD IODIDE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；25% PEG 3350, 0.2M KI	Resolution 1.37 Å R-free 0.224

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7SKY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 35–269（235 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 35–269（235 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 36–269（234 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 36–269（234 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
7SKI Pertussis toxin in complex with PJ34 Deposited 2021-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–214（179 aa）	Mutation：C41S	P34 N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.15M NaCl, 0.1M Tris(hydroxymethyl)aminomethane pH 8.0, 8% w/v PEG 8000	Resolution 1.10 Å R-free 0.178
7SKI Pertussis toxin in complex with PJ34 Deposited 2021-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–214（179 aa）	Mutation：C41S	P34 N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.15M NaCl, 0.1M Tris(hydroxymethyl)aminomethane pH 8.0, 8% w/v PEG 8000	Resolution 1.10 Å R-free 0.178
7SKK pertussis toxin in complex with ADPR and Nicotinamide Deposited 2021-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–216（181 aa）	Mutation：C41S	NCA NICOTINAMIDE × 1 AR6 [(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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.5M (NH4)2SO4 and 0.1M HEPES pH 7	Resolution 1.65 Å R-free 0.198
7SKK pertussis toxin in complex with ADPR and Nicotinamide Deposited 2021-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–216（181 aa）	Mutation：C41S	NCA NICOTINAMIDE × 1 AR6 [(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 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.5M (NH4)2SO4 and 0.1M HEPES pH 7	Resolution 1.65 Å R-free 0.198
7SKK pertussis toxin in complex with ADPR and Nicotinamide Deposited 2021-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–216（181 aa）	Mutation：C41S	NCA NICOTINAMIDE × 1 AR6 [(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 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.5M (NH4)2SO4 and 0.1M HEPES pH 7	Resolution 1.65 Å R-free 0.198
7SKK pertussis toxin in complex with ADPR and Nicotinamide Deposited 2021-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 36–216（181 aa）	Mutation：C41S	NCA NICOTINAMIDE × 1 AR6 [(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 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.5M (NH4)2SO4 and 0.1M HEPES pH 7	Resolution 1.65 Å R-free 0.198
7SNE Pertussis toxin S1 subunit bound to BaAD Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–216（181 aa）	Mutation：C41S	9XR [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2M LiCl, 14% w/v PEG 3350	Resolution 1.00 Å R-free 0.219
7SNE Pertussis toxin S1 subunit bound to BaAD Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–216（181 aa）	Mutation：C41S	9XR [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2M LiCl, 14% w/v PEG 3350	Resolution 1.00 Å R-free 0.219
7SNE Pertussis toxin S1 subunit bound to BaAD Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–216（181 aa）	Mutation：C41S	9XR [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2M LiCl, 14% w/v PEG 3350	Resolution 1.00 Å R-free 0.219
7SNE Pertussis toxin S1 subunit bound to BaAD Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 36–216（181 aa）	Mutation：C41S	9XR [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2M LiCl, 14% w/v PEG 3350	Resolution 1.00 Å R-free 0.219
7U6Z Pertussis toxin E129D NAD Deposited 2022-03-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–216（181 aa）	Not recorded	IOD IODIDE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2M KI, 25% PEG3350	Resolution 1.30 Å R-free 0.214
7U6Z Pertussis toxin E129D NAD Deposited 2022-03-06	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–216（181 aa）	Not recorded	IOD IODIDE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2M KI, 25% PEG3350	Resolution 1.30 Å R-free 0.214
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 35–269（235 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å

7 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

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	7sky
Deposition date deposition_date	2021-10-21
Structure title title	Pertussis toxin S1 bound to NAD+
Keywords keywords	Whooping cough, Pertussis, pertussis toxin, S1, ADP ribosyltransferase, toxin, TRANSFERASE; TOXIN, TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.26 Å
Radius of gyration Rg (electron density) rg_electron	31.80 Å
Forward intensity I(0) i0	134485000.00
Molecular weight molecular_weight	83757.0 kDa
Excluded volume excluded_volume	100810 Å³
Envelope volume envelope_volume	133400 Å³
Hydration-shell volume shell_volume	35574 Å³
Envelope diameter envelope_diameter	114.3 Å
Shell Rg shell_rg	37.64 Å
Envelope Rg envelope_rg	31.95 Å
Shape Rg shape_rg	31.79 Å
Total Rg total_rg	32.27 Å
Total atoms total_atoms	5885
Residues n_residues	717
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.7 Å
Rg (real space) rg_real	32.26 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	1.3450e+08
I(0) uncertainty (real space) i0_real_error	2.4820e+06
Rg (reciprocal space) rg_reciprocal	32.26 Å
I(0) (reciprocal space) i0_reciprocal	134500000.0000
Solution quality estimate total_estimate	0.8810
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	40.3 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13800000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.919

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Pertussis toxin subunit 1
Molecular weight formula_weight	20741.4 kDa
EC 编号 ec_number	2.4.2.-, 2.4.2.30
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D
Atom count atom_count	6564

GPGDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRR

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	679

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7skyA01
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	7skyB01
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	7skyC01
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	7skyD01
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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8. Citations (1)

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Unit-cell length a length_a	34.600 Å
Unit-cell length b length_b	68.250 Å
Unit-cell length c length_c	71.670 Å
Unit-cell angle α angle_alpha	90.73 °
Unit-cell angle β angle_beta	90.27 °
Unit-cell angle γ angle_gamma	91.45 °
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	1.370 Å
Low-resolution limit resolution_low	24.601 Å
R factor r_factor	0.2031
R_work r_work	0.2020
R_free r_free	0.2243

fit	/app/data/saxs_computation/sk/7sky/7sky.fit
pddf	/app/data/pr_computation/sk/7sky/7sky.pr.out
profile	/app/data/saxs_computation/sk/7sky/7sky.dat

Pertussis toxin S1 bound to NAD+

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction