SAXSdb — 1pvj

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

pyrogenic exotoxin B

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	(3R)-3-{[(BENZYLOXY)CARBONYL]AMINO}-2-OXO-4-PHENYLBUTANE-1-DIAZONIUM × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPEB_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–368； UniProt 31–398 Author chain B； PDBConstruct 1–368； UniProt 31–398 Author chain C； PDBConstruct 1–368； UniProt 31–398 Author chain D； PDBConstruct 1–368； UniProt 31–398

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	1pvj
Deposition date deposition_date	2003-06-27
Structure title title	Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex
Keywords keywords	Streptococcus pyogenes exotoxin(SpeB), Z-F-CH2N2- benzyloxycarbonyl phenylalanyl alanyl diazomethane., TOXIN; 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.

1pvj__assembly_1__model_1

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

Download this curve (.dat)

1pvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.40 Å
Rg (electron density)	38.27 Å
Total Rg	38.54 Å
Atom count	10500
Residues	1356
Excluded volume	184660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pvj__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	pyrogenic exotoxin B
Molecular weight formula_weight	40021.3 kDa
EC 编号 ec_number	3.4.22.10
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11052

FARNEKEAKDSAITFIQKSAAIKAGARSAEDIKLDKVNLGGELSGSNMYVYNISTGGFVIVSGDKRSPEILGYSTSGSFDANGKENIASFMESYVEQIKENKKLDTTYAGTAEIKQPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRGDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGADGFNGYQSAVVGIKP

Entity 2 Entity 2 non-polymer

Description description	(3R)-3-{[(BENZYLOXY)CARBONYL]AMINO}-2-OXO-4-PHENYLBUTANE-1-DIAZONIUM
Molecular weight formula_weight	324.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	552

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pvja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1pvjb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1pvjc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1pvjd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

CATH v4.4 (8 domains)

Domain ID domain_id	1pvjA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1pvjA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

Domain ID domain_id	1pvjB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1pvjB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

Domain ID domain_id	1pvjC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1pvjC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

Domain ID domain_id	1pvjD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1pvjD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

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Unit-cell length a length_a	95.769 Å
Unit-cell length b length_b	119.495 Å
Unit-cell length c length_c	144.083 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	—
R_work r_work	0.2270
R_free r_free	0.2880

Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex

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

pyrogenic exotoxin B

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

1pvj__assembly_1__model_1

1pvj__assembly_1__model_1 | I(q)

1pvj__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex

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

pyrogenic exotoxin B

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

1pvj__assembly_1__model_1

1pvj__assembly_1__model_1 | I(q)

1pvj__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)