5imy

Trapped Toxin

Method: X-RAY DIFFRACTION

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

Vaginolysin

Gardnerella vaginalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CD59 glycoprotein × 2 （P13987） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2YGA4_GARVA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–490； UniProt 29–516 Author chain B； PDBConstruct 3–490； UniProt 29–516

CD59 glycoprotein

Homo sapiens

UniProt P13987

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Vaginolysin × 2 （B2YGA4） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD59_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–78； UniProt 26–102 Author chain D； PDBConstruct 2–78； UniProt 26–102

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	5imy
Deposition date deposition_date	2016-03-07
Structure title title	Trapped Toxin
Keywords keywords	toxin-toxin receptor complex; toxin/toxin receptor
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.

5imy__assembly_1__model_1

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

Download this curve (.dat)

5imy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5imy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.63 Å
Rg (electron density)	39.01 Å
Total Rg	39.15 Å
Atom count	17058
Residues	1102
Excluded volume	152630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5imy__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	Vaginolysin
Molecular weight formula_weight	54213.4 kDa
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	17217

SNAHMAPSAKDSEPATSCAAKKDSLNNYLWDLQYDKTNILARHGETIENKFSSDSFNKNGEFVVVEHQKKNITNTTSNLSVTSANDDRVYPGALFRADKNLMDNMPSLISANRAPITLSVDLPGFHGGESAVTVQRPTKSSVTSAVNGLVSKWNAQYGASHHVAARMQYDSASAQSMNQLKAKFGADFAKIGVPLKIDFDAVHKGEKQTQIVNFKQTYYTVSVDAPDSPADFFAPCTTPDSLKNRGVDNKRPPVYVSNVAYGRSMYVKFDTTSKSTDFQAAVEAAIKGVEIKPNTEFHRILQNTSVCAVILGGSANGAAKVCTGNIDTLKALIQEGANLSTSSPAVPIAYTTSFVKDNEVATLQSNSDYIETKVSSYRNGYLTLDHRGAYVARYYIYWDEYGTEIDGTPYVRSRAWEGNGKYRTAHFNTTIQFKGNVRNLRIKLVEKTGLVWEPWRTVYDRSDLPLVRQRTISNWGTTLWPRVAETVKND

Source Source

Source organism organism	Gardnerella vaginalis
NCBI taxonomy ID ncbi_taxonomy_id	2702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CD59 glycoprotein
Molecular weight formula_weight	9101.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENELTYYCCKKDLCNFNEQLEN

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5imya1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d5imya2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

Domain ID domain_id	d5imyb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d5imyb2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

Domain ID domain_id	d5imyc1
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d5imyc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5imyd1
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d5imyd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

Domain ID domain_id	5imyA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	5imyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5imyA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	5imyA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	5imyB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	5imyB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5imyB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	5imyB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	5imyC00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	5imyD00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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Unit-cell length a length_a	81.894 Å
Unit-cell length b length_b	141.713 Å
Unit-cell length c length_c	106.732 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	42.639 Å
R factor r_factor	0.2354
R_work r_work	0.2340
R_free r_free	0.2759

Trapped Toxin

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

Vaginolysin

State in the Current Structure

Other States of the Same Protein in the Database

CD59 glycoprotein

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

5imy__assembly_1__model_1

5imy__assembly_1__model_1 | I(q)

5imy__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) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Trapped Toxin

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

Vaginolysin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CD59 glycoprotein

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

5imy__assembly_1__model_1

5imy__assembly_1__model_1 | I(q)

5imy__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) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)