1t5r

STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS

Method: X-RAY DIFFRACTION

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

LukS-PV

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O80066_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 29–312 Author chain B； PDBConstruct 1–284； UniProt 29–312 Author chain C； PDBConstruct 1–284； UniProt 29–312 Author chain D； PDBConstruct 1–284； UniProt 29–312 Author chain E； PDBConstruct 1–284； UniProt 29–312 Author chain F； PDBConstruct 1–284； UniProt 29–312 Author chain G； PDBConstruct 1–284； UniProt 29–312 Author chain H； PDBConstruct 1–284； UniProt 29–312

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	1t5r
Deposition date deposition_date	2004-05-05
Structure title title	STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
Keywords keywords	BI-COMPONENT LEUCOTOXIN, PORE-FORMING TOXIN, STAPHYLOCOCCUS AUREUS, S COMPONENT LEUCOCIDIN, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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.

1t5r__assembly_1__model_1

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

Download this curve (.dat)

1t5r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t5r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.58 Å
Rg (electron density)	50.41 Å
Total Rg	50.49 Å
Atom count	17092
Residues	2151
Excluded volume	298460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t5r__assembly_1__model_1`	octameric （8）	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 (2)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1t5ra_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5rb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5rc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5rd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5re_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5rf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5rg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d1t5rh_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

CATH v4.4 (8 domains)

Domain ID domain_id	1t5rA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rD00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rE00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rF00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rG00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	1t5rH00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

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Unit-cell length a length_a	94.850 Å
Unit-cell length b length_b	94.850 Å
Unit-cell length c length_c	306.110 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	32

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	35.500 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2470

Description description	LukS-PV
Molecular weight formula_weight	32355.6 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	17913

STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS

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

LukS-PV

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

1t5r__assembly_1__model_1

1t5r__assembly_1__model_1 | I(q)

1t5r__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	821

STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS

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

LukS-PV

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

1t5r__assembly_1__model_1

1t5r__assembly_1__model_1 | I(q)

1t5r__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)