3cl5

Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid

Method: X-RAY DIFFRACTION

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

Hemagglutinin-esterase

Bovine coronavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 2 POTASSIUM ION × 2 ACETIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEMA_CVBM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 19–388

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	3cl5
Deposition date deposition_date	2008-03-18
Structure title title	Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid
Keywords keywords	SGNH-hydrolase fold, Swiss roll, Envelope protein, Glycoprotein, Hemagglutinin, Membrane, Transmembrane, Virion, 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.

3cl5__assembly_1__model_1

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

Download this curve (.dat)

3cl5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cl5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.19 Å
Rg (electron density)	28.09 Å
Total Rg	28.84 Å
Atom count	5982
Residues	716
Excluded volume	105530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cl5__assembly_1__model_1`	dimeric （2）	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 (7)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin-esterase
Molecular weight formula_weight	42630.2 kDa
EC 编号 ec_number	3.1.1.53
Mutation mutation	S40A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3272

FDNPPTNVVSHLNGDWFLFGDARSDCNHVVNTNPRNYSYMDLNPALCDSGKISSKAGNSIFRSFHFTDFYNYTGEGQQIIFYEGVNFTPYHAFKCTTSGSNDIWMQNKGLFYTQVYKNMAVYRSLTFVNVPYVYNGSAQSTALCKSGSLVLNNPAYIAREANFGDYYYKVEADFYLSGCDEYIVPLCIFNGKFLSNTKYYDDSQYYFNKDTGVIYGLNSTETITTGFDFNCHYLVLPSGNYLAISNELLLTVPTKAICLNKRKDFTPVQVVDSRWNNARQSDNMTAVACQPPYCYFRNSTTNYVGVYDINHGDAGFTSILSGLLYDSPCFSQQGVFRYDNVSSVWPLYSYGRCPTAADINTPDVPICVYDSDPLVPR

Source Source

Source organism organism	Bovine coronavirus
Common name common_name	strain Mebus
NCBI taxonomy ID ncbi_taxonomy_id	11128
Host organism host_organism	Homo Sapiens

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
Molecular weight formula_weight	407.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	281

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Unit-cell length a length_a	89.240 Å
Unit-cell length b length_b	89.240 Å
Unit-cell length c length_c	280.380 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1712
R_work r_work	0.1703
R_free r_free	0.1883

Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid

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

Hemagglutinin-esterase

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

3cl5__assembly_1__model_1

3cl5__assembly_1__model_1 | I(q)

3cl5__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid

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

Hemagglutinin-esterase

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

3cl5__assembly_1__model_1

3cl5__assembly_1__model_1 | I(q)

3cl5__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)