SAXSdb — 5iyt

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

EV-B93 main protease 3C

Echovirus 1 (strain Human/Egypt/Farouk/1951)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-butanamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_EC01F
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–185； UniProt 1540–1722 Author chain B； PDBConstruct 3–185； UniProt 1540–1722

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	5iyt
Deposition date deposition_date	2016-03-24
Structure title title	Complex structure of EV-B93 main protease 3C with N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-2Z-butenamide
Keywords keywords	3C main protease, Enterovirus B93, covalent inhibitor, hydrolase; HYDROLASE
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.

5iyt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5iyt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5iyt__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.62 Å
Rg (electron density)	15.22 Å
Total Rg	16.38 Å
Atom count	1439
Residues	182
Excluded volume	25776 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5iyt__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5iyt__assembly_2__model_1`	monomeric （1）	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	EV-B93 main protease 3C
Molecular weight formula_weight	21395.5 kDa
EC 编号 ec_number	3.4.22.29,3.6.1.15,3.4.22.28
Mutation mutation	M137V
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	3076

MKGPAFEFAVAMMKRNASTVKTEYGEFTMLGIYDRWAVLPRHAKPGPTILMNDQEVGVLDAKELVDKDGTNLELTLLKLNRNEKFRDIRGFLAREEVEVNEAVLAINTSKFPNMYIPVGQVTDYGFLNLGGTPTKRMLVYNFPTRAGQCGGVLMSTGKVLGIHVGGNGHQGFSAALLRHYFNEEQHHHHHH

Source Source

Source organism organism	Echovirus 1 (strain Human/Egypt/Farouk/1951)
Common name common_name	E-1
NCBI taxonomy ID ncbi_taxonomy_id	103908
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-butanamide
Molecular weight formula_weight	322.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5iyta_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

Domain ID domain_id	d5iytb_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

CATH v4.4 (4 domains)

Domain ID domain_id	5iytA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	5iytA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	5iytB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	5iytB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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Unit-cell length a length_a	57.460 Å
Unit-cell length b length_b	52.330 Å
Unit-cell length c length_c	62.270 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.73 °
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	1.730 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1889
R_work r_work	0.1874
R_free r_free	0.2173

Complex structure of EV-B93 main protease 3C with N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-2Z-butenamide

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

EV-B93 main protease 3C

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

5iyt__assembly_2__model_1

5iyt__assembly_2__model_1 | I(q)

5iyt__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Complex structure of EV-B93 main protease 3C with N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-2Z-butenamide

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

EV-B93 main protease 3C

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

5iyt__assembly_2__model_1

5iyt__assembly_2__model_1 | I(q)

5iyt__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)