4hx3

Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin

Method: X-RAY DIFFRACTION

▼

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

Extracellular small neutral protease

Streptomyces caespitosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Neutral proteinase inhibitor ScNPI × 2 （Q9FDS0） ZINC ION × 2 GLYCEROL × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Neutral proteinase inhibitor ScNPI × 2 （Q9FDS0） ZINC ION × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Neutral proteinase inhibitor ScNPI × 2 （Q9FDS0） ZINC ION × 2 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNPA_STRCS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–134； UniProt 2–132 Author chain C； PDBConstruct 4–134； UniProt 2–132 Author chain E； PDBConstruct 4–134； UniProt 2–132 Author chain G； PDBConstruct 4–134； UniProt 2–132 Author chain I； PDBConstruct 4–134； UniProt 2–132 Author chain K； PDBConstruct 4–134； UniProt 2–132

Neutral proteinase inhibitor ScNPI

Streptomyces caespitosus

UniProt Q9FDS0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Extracellular small neutral protease × 2 （P56406） ZINC ION × 2 GLYCEROL × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Extracellular small neutral protease × 2 （P56406） ZINC ION × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Extracellular small neutral protease × 2 （P56406） ZINC ION × 2 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9FDS0_STRCS
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–114； UniProt 29–141 Author chain D； PDBConstruct 2–114； UniProt 29–141 Author chain F； PDBConstruct 2–114； UniProt 29–141 Author chain H； PDBConstruct 2–114； UniProt 29–141 Author chain J； PDBConstruct 2–114； UniProt 29–141 Author chain L； PDBConstruct 2–114； UniProt 29–141

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4hx3
Deposition date deposition_date	2012-11-09
Structure title title	Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin
Keywords keywords	Streptomyces subtilisin inhibitor fold, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4hx3__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4hx3__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4hx3__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	26.05 Å
Rg (electron density)	25.34 Å
Total Rg	26.08 Å
Atom count	3704
Residues	491
Excluded volume	64170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4hx3__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4hx3__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4hx3__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Extracellular small neutral protease
Molecular weight formula_weight	14571.6 kDa
EC 编号 ec_number	3.4.24.77
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	11334

GPMVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG

Source Source

Source organism organism	Streptomyces caespitosus
NCBI taxonomy ID ncbi_taxonomy_id	53502
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Neutral proteinase inhibitor ScNPI
Molecular weight formula_weight	11923.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

GSAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF

Source Source

Source organism organism	Streptomyces caespitosus
NCBI taxonomy ID ncbi_taxonomy_id	53502
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	275

▼

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

Domain ID domain_id	d4hx3a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.1 — Zinc protease

Domain ID domain_id	d4hx3a2
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	d4hx3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

Domain ID domain_id	d4hx3c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.1 — Zinc protease

Domain ID domain_id	d4hx3c2
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	d4hx3d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

Domain ID domain_id	d4hx3e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.1 — Zinc protease

Domain ID domain_id	d4hx3e2
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	d4hx3f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

Domain ID domain_id	d4hx3g1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.1 — Zinc protease

Domain ID domain_id	d4hx3g2
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	d4hx3h1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

Domain ID domain_id	d4hx3h2
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	d4hx3i1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.1 — Zinc protease

Domain ID domain_id	d4hx3i2
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	d4hx3j_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

Domain ID domain_id	d4hx3k1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.1 — Zinc protease

Domain ID domain_id	d4hx3k2
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	d4hx3l_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	4hx3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4hx3B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

Domain ID domain_id	4hx3C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4hx3D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

Domain ID domain_id	4hx3E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4hx3F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

Domain ID domain_id	4hx3G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4hx3H00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

Domain ID domain_id	4hx3I00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4hx3J00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

Domain ID domain_id	4hx3K00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4hx3L00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

▶

Unit-cell length a length_a	116.540 Å
Unit-cell length b length_b	121.810 Å
Unit-cell length c length_c	130.670 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	24

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	43.490 Å
R factor r_factor	0.1957
R_work r_work	0.1950
R_free r_free	0.2423

Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin

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

Extracellular small neutral protease

State in the Current Structure

Other States of the Same Protein in the Database

Neutral proteinase inhibitor ScNPI

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

4hx3__assembly_3__model_1

4hx3__assembly_3__model_1 | I(q)

4hx3__assembly_3__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) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin

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

Extracellular small neutral 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

Neutral proteinase inhibitor ScNPI

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

4hx3__assembly_3__model_1

4hx3__assembly_3__model_1 | I(q)

4hx3__assembly_3__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) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. Citations (1)