SAXSdb — 7ski

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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 A； UniProt 36–214	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 36–214	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

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 7SKI	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
7SKK pertussis toxin in complex with ADPR and Nicotinamide Deposited 2021-10-21	Different construct 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 construct 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 construct 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 construct 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
7SKY Pertussis toxin S1 bound to NAD+ Deposited 2021-10-21	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 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, HANGING DROP；295 K；25% PEG 3350, 0.2M KI	Resolution 1.37 Å R-free 0.224
7SKY Pertussis toxin S1 bound to NAD+ Deposited 2021-10-21	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 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, HANGING DROP；295 K；25% PEG 3350, 0.2M KI	Resolution 1.37 Å R-free 0.224
7SKY Pertussis toxin S1 bound to NAD+ Deposited 2021-10-21	Different construct 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）	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
7SKY Pertussis toxin S1 bound to NAD+ Deposited 2021-10-21	Different construct 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）	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
7SNE Pertussis toxin S1 subunit bound to BaAD Deposited 2021-10-28	Different construct 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 construct 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 construct 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 construct 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 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 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 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 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 mutation/modification 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 19 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 4–182； UniProt 36–214 Author chain B； PDBConstruct 4–182； UniProt 36–214

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	7ski
Deposition date deposition_date	2021-10-20
Structure title title	Pertussis toxin in complex with PJ34
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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.61 Å
Radius of gyration Rg (electron density) rg_electron	21.45 Å
Forward intensity I(0) i0	31777800.00
Molecular weight molecular_weight	40535.0 kDa
Excluded volume excluded_volume	49470 Å³
Envelope volume envelope_volume	60377 Å³
Hydration-shell volume shell_volume	23312 Å³
Envelope diameter envelope_diameter	69.3 Å
Shell Rg shell_rg	28.03 Å
Envelope Rg envelope_rg	21.53 Å
Shape Rg shape_rg	21.42 Å
Total Rg total_rg	22.31 Å
Total atoms total_atoms	2874
Residues n_residues	354
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	68.4 Å
Rg (real space) rg_real	22.48 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.1780e+07
I(0) uncertainty (real space) i0_real_error	3.8770e+05
Rg (reciprocal space) rg_reciprocal	22.52 Å
I(0) (reciprocal space) i0_reciprocal	31780000.0000
Solution quality estimate total_estimate	0.9148
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.0 Å
Skewness Skewness skewness	0.114
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4624000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Pertussis toxin subunit 1
Molecular weight formula_weight	20411.0 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3317

GPGDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSSQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTS

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	N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
Molecular weight formula_weight	295.3 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	422

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8. Citations (1)

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Unit-cell length a length_a	59.369 Å
Unit-cell length b length_b	42.541 Å
Unit-cell length c length_c	72.775 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.099 Å
Low-resolution limit resolution_low	21.831 Å
R factor r_factor	0.1714
R_work r_work	0.1711
R_free r_free	0.1784

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

Pertussis toxin in complex with PJ34

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