6u4p

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus

Method: X-RAY DIFFRACTION

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

Alpha-hemolysin

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 7	fos-choline-14 × 14 SULFATE ION × 33 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLA_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–293； UniProt 27–319 Author chain B； PDBConstruct 1–293； UniProt 27–319 Author chain C； PDBConstruct 1–293； UniProt 27–319 Author chain D； PDBConstruct 1–293； UniProt 27–319 Author chain E； PDBConstruct 1–293； UniProt 27–319 Author chain F； PDBConstruct 1–293； UniProt 27–319 Author chain G； PDBConstruct 1–293； UniProt 27–319

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	6u4p
Deposition date deposition_date	2019-08-26
Structure title title	Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
Keywords keywords	alpha-toxin, PVL, Leukocidins, MRSA, 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.

6u4p__assembly_1__model_1

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

Download this curve (.dat)

6u4p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6u4p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.64 Å
Rg (electron density)	38.41 Å
Total Rg	38.96 Å
Atom count	16700
Residues	2051
Excluded volume	293320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6u4p__assembly_1__model_1`	heptameric （7）	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 (4)

Entity 1 Entity 1 polymer

Description description	Alpha-hemolysin
Molecular weight formula_weight	33222.9 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	16814

ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMAKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWGPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	fos-choline-14
Molecular weight formula_weight	380.5 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	33

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d6u4pa_
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	d6u4pb_
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	d6u4pc_
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	d6u4pd_
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	d6u4pe_
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	d6u4pf_
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	d6u4pg_
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 (7 domains)

Domain ID domain_id	6u4pA00
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	6u4pB00
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	6u4pC00
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	6u4pD00
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	6u4pE00
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	6u4pF00
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	6u4pG00
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	151.174 Å
Unit-cell length b length_b	134.616 Å
Unit-cell length c length_c	130.697 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	37.800 Å
R factor r_factor	0.2139
R_work r_work	0.2121
R_free r_free	0.2495

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus

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

Alpha-hemolysin

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

6u4p__assembly_1__model_1

6u4p__assembly_1__model_1 | I(q)

6u4p__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus

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

Alpha-hemolysin

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

6u4p__assembly_1__model_1

6u4p__assembly_1__model_1 | I(q)

6u4p__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)