SAXSdb — 1y4h

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

cysteine protease

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	cysteine protease inhibitor × 1 （Q9EYW6） CHLORIDE ION × 3 SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	cysteine protease inhibitor × 1 （Q9EYW6） CHLORIDE ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	cysteine protease inhibitor × 2 （Q9EYW6） CHLORIDE ION × 4 SULFATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSPB_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–188； UniProt 220–393 Author chain B； PDBConstruct 15–188； UniProt 220–393

cysteine protease inhibitor

Staphylococcus aureus

UniProt Q9EYW6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	cysteine protease × 1 （Q70UQ8） CHLORIDE ION × 3 SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	cysteine protease × 1 （Q70UQ8） CHLORIDE ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	cysteine protease × 2 （Q70UQ8） CHLORIDE ION × 4 SULFATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSPC_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–109； UniProt 1–109 Author chain D； PDBConstruct 1–109； UniProt 1–109

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	1y4h
Deposition date deposition_date	2004-11-30
Structure title title	Wild type staphopain-staphostatin complex
Keywords keywords	cysteine protease, inhibitor, staphopain B, staphostatin B, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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.

1y4h__assembly_1__model_1

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

Download this curve (.dat)

1y4h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y4h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.36 Å
Rg (electron density)	20.27 Å
Total Rg	21.20 Å
Atom count	2330
Residues	282
Excluded volume	40779 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y4h__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1y4h__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1y4h__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	cysteine protease
Molecular weight formula_weight	21550.6 kDa
EC 编号 ec_number	3.4.22.-
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	4813

MGSSHHHHHHSQDPDQVQYENTLKNFKIREQQFDNSWCAGFSMAALLNATKNTDTYNAHDIMRTLYPEVSEQDLPNCATFPNQMIEYGKSQGRDIHYQEGVPSYNQVDQLTKDNVGIMILAQSVSQNPNDPHLGHALAVVGNAKINDQEKLIYWNPWDTELSIQDADSSLLHLSFNRDYNWYGSMIGY

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	cysteine protease inhibitor
Molecular weight formula_weight	12930.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MYQLQFINLVYDTTKLTHLEQTNINLFIGNWSNHQLQKSICIRHGDDTSHNQYHILFIDTAHQRIKFSSFDNEEIIYILDYDDTQHILMQTSSKQGIGTSRPIVYERLV

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1y4ha1
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	d1y4hb_
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	d1y4hc_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.2 — beta-Barrel protease inhibitors
Family Family family	b.61.2.2 — Staphostatin

Domain ID domain_id	d1y4hd_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.2 — beta-Barrel protease inhibitors
Family Family family	b.61.2.2 — Staphostatin

CATH v4.4 (4 domains)

Domain ID domain_id	1y4hA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	1y4hB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	1y4hC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	310 — Staphostatins
Homologous superfamily homologous superfamily	10 — beta-Barrel protease inhibitors

Domain ID domain_id	1y4hD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	310 — Staphostatins
Homologous superfamily homologous superfamily	10 — beta-Barrel protease inhibitors

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Unit-cell length a length_a	57.948 Å
Unit-cell length b length_b	77.520 Å
Unit-cell length c length_c	84.891 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.10 °
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	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1897
R_work r_work	0.1883
R_free r_free	0.2167

Wild type staphopain-staphostatin complex

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

cysteine protease

State in the Current Structure

Other States of the Same Protein in the Database

cysteine protease inhibitor

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

1y4h__assembly_1__model_1

1y4h__assembly_1__model_1 | I(q)

1y4h__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (5)

Wild type staphopain-staphostatin complex

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

cysteine protease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

cysteine protease inhibitor

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

1y4h__assembly_1__model_1

1y4h__assembly_1__model_1 | I(q)

1y4h__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (5)