6e7g

Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus

Method: X-RAY DIFFRACTION

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

Hemagglutinin HA1 chain

Influenza A virus (A/Viet Nam/1203/2004(H5N1))

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 4	Hemagglutinin HA2 chain × 3 （Q6DQ18） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5EP31_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–334； UniProt 17–346 Author chain C； PDBConstruct 5–334； UniProt 17–346 Author chain E； PDBConstruct 5–334； UniProt 17–346

Hemagglutinin HA2 chain

Influenza A virus (A/Viet Nam/1203/2004(H5N1))

UniProt Q6DQ18

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 4	Hemagglutinin HA1 chain × 3 （Q5EP31） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEMA_I02A6
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–174； UniProt 339–512 Author chain D； PDBConstruct 1–174； UniProt 339–512 Author chain F； PDBConstruct 1–174； UniProt 339–512

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6e7g
Deposition date deposition_date	2018-07-26
Structure title title	Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus
Keywords keywords	Influenza virus, hemagglutinin, HA, H5N1, A/Viet Nam/1203/2004, Receptor specificity, VIRAL PROTEIN; VIRAL PROTEIN
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.

6e7g__assembly_1__model_1

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

Download this curve (.dat)

6e7g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6e7g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.87 Å
Rg (electron density)	41.51 Å
Total Rg	41.63 Å
Atom count	11548
Residues	1422
Excluded volume	203680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6e7g__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1 chain
Molecular weight formula_weight	37855.9 kDa
Mutation mutation	Y161A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	11548

ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTAPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

Source Source

Source organism organism	Influenza A virus (A/Viet Nam/1203/2004(H5N1))
NCBI taxonomy ID ncbi_taxonomy_id	284218
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2 chain
Molecular weight formula_weight	20414.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR

Source Source

Source organism organism	Influenza A virus (A/Viet Nam/1203/2004(H5N1))
NCBI taxonomy ID ncbi_taxonomy_id	284218
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 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	3

Entity 4 Entity 4 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 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	2

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6e7ga_
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.19.1.0 — automated matches

Domain ID domain_id	d6e7gb_
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.3.1.0 — automated matches

Domain ID domain_id	d6e7gc_
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.19.1.0 — automated matches

Domain ID domain_id	d6e7gd_
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.3.1.0 — automated matches

Domain ID domain_id	d6e7ge_
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.19.1.0 — automated matches

Domain ID domain_id	d6e7gf_
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.3.1.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id	6e7gA01
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	6e7gA02
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	6e7gB00
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	6e7gC01
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	6e7gC02
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	6e7gD00
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	6e7gE01
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	6e7gE02
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	6e7gF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	66.214 Å
Unit-cell length b length_b	231.136 Å
Unit-cell length c length_c	70.864 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.094 Å
Low-resolution limit resolution_low	37.814 Å
R factor r_factor	0.2241
R_work r_work	0.2217
R_free r_free	0.2685

Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus

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

Hemagglutinin HA1 chain

State in the Current Structure

Other States of the Same Protein in the Database

Hemagglutinin HA2 chain

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

6e7g__assembly_1__model_1

6e7g__assembly_1__model_1 | I(q)

6e7g__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus

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

Hemagglutinin HA1 chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin HA2 chain

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

6e7g__assembly_1__model_1

6e7g__assembly_1__model_1 | I(q)

6e7g__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)