SAXSdb — 2q6f

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

Infectious bronchitis virus (IBV) main protease

Infectious bronchitis virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	;N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE ; × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3Y5H1_9CORO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–309； UniProt 1–307 Author chain B； PDBConstruct 3–309； UniProt 1–307

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	2q6f
Deposition date deposition_date	2007-06-05
Structure title title	Crystal structure of infectious bronchitis virus (IBV) main protease in complex with a Michael acceptor inhibitor N3
Keywords keywords	coronavirus; IBV; main protease; 3C-Like proteinase; Michael acceptor 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.

2q6f__assembly_1__model_1

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

Download this curve (.dat)

2q6f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2q6f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.54 Å
Rg (electron density)	25.36 Å
Total Rg	26.17 Å
Atom count	4620
Residues	595
Excluded volume	82273 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q6f__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Infectious bronchitis virus (IBV) main protease
Molecular weight formula_weight	33635.9 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	5039

GSSGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDSIYCPRHVLGKFSGDQWGDVLNLANNHEFEVVTQNGVTLNVVSRRLKGAVLILQTAVANAETPKYKFVKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSQPKWLESTTVSIEDYNRWASDNGFTPFSTSTAITKLSAITGVDVCKLLRTIMVKSAQWGSDPILGQYNFEDELTPESVFNQVGGVRLQ

Source Source

Source organism organism	Infectious bronchitis virus
NCBI taxonomy ID ncbi_taxonomy_id	11120
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	;N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE ;
Molecular weight formula_weight	680.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XAVLXX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	419

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q6fa_
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.47.1.0 — automated matches

Domain ID domain_id	d2q6fb_
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.47.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2q6fA01
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	2q6fA02
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	2q6fA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1840 — main proteinase (3clpro) structure, domain 3
Homologous superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

Domain ID domain_id	2q6fB01
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	2q6fB02
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	2q6fB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1840 — main proteinase (3clpro) structure, domain 3
Homologous superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

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Unit-cell length a length_a	53.175 Å
Unit-cell length b length_b	54.502 Å
Unit-cell length c length_c	66.719 Å
Unit-cell angle α angle_alpha	111.06 °
Unit-cell angle β angle_beta	104.31 °
Unit-cell angle γ angle_gamma	91.33 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2420

Crystal structure of infectious bronchitis virus (IBV) main protease in complex with a Michael acceptor inhibitor N3

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

Infectious bronchitis virus (IBV) main protease

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

2q6f__assembly_1__model_1

2q6f__assembly_1__model_1 | I(q)

2q6f__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of infectious bronchitis virus (IBV) main protease in complex with a Michael acceptor inhibitor N3

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

Infectious bronchitis virus (IBV) main 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2q6f__assembly_1__model_1

2q6f__assembly_1__model_1 | I(q)

2q6f__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)