3znk

H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)

Method: X-RAY DIFFRACTION

▼

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

HAEMAGGLUTININ

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 6 其他Polymer 3	N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6DQ34_9INFA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 17–342 Author chain C； PDBConstruct 1–326； UniProt 17–342 Author chain E； PDBConstruct 1–326； UniProt 17–342 Author chain B； PDBConstruct 1–166； UniProt 347–512 Author chain D； PDBConstruct 1–166； UniProt 347–512 Author chain F； PDBConstruct 1–166； UniProt 347–512

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	3znk
Deposition date deposition_date	2013-02-15
Structure title title	H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)
Keywords keywords	;VIRAL PROTEIN, SIALIC ACID, GLYCOPROTEIN, VIRUS RECEPTOR, SULFATED SIALOSIDE, FUCOSYLATED SIALOSIDE, SULFATION, FUCOSYLATION, AVIAN FLU, SIALYLLACTOSAMINE, LEWIS X ;; VIRAL PROTEIN
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.

3znk__assembly_1__model_1

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

Download this curve (.dat)

3znk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3znk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.93 Å
Rg (electron density)	41.39 Å
Total Rg	41.55 Å
Atom count	11916
Residues	1452
Excluded volume	210060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3znk__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	HAEMAGGLUTININ
Molecular weight formula_weight	36950.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	12112

DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRETR

Entity 2 Entity 2 polymer

Description description	HAEMAGGLUTININ
Molecular weight formula_weight	19098.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA

Entity 3 Entity 3 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose
Molecular weight formula_weight	754.7 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 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	9

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

▼

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3znka_
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.2 — Influenza hemagglutinin headpiece

Domain ID domain_id	d3znkb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
Family Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

Domain ID domain_id	d3znkc_
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.2 — Influenza hemagglutinin headpiece

Domain ID domain_id	d3znkd_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
Family Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

Domain ID domain_id	d3znke_
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.2 — Influenza hemagglutinin headpiece

Domain ID domain_id	d3znkf_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
Family Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

CATH v4.4 (9 domains)

Domain ID domain_id	3znkA01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

Domain ID domain_id	3znkA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	3znkB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3znkC01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

Domain ID domain_id	3znkC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	3znkD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3znkE01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

Domain ID domain_id	3znkE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	3znkF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	175.340 Å
Unit-cell length b length_b	101.230 Å
Unit-cell length c length_c	160.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.710 Å
Low-resolution limit resolution_low	43.060 Å
R factor r_factor	0.2229
R_work r_work	0.2221
R_free r_free	0.2365

H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)

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

HAEMAGGLUTININ

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

3znk__assembly_1__model_1

3znk__assembly_1__model_1 | I(q)

3znk__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)

H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)

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

HAEMAGGLUTININ

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

3znk__assembly_1__model_1

3znk__assembly_1__model_1 | I(q)

3znk__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)