5w6r

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)

Method: X-RAY DIFFRACTION

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

Hemagglutinin

Influenza A virus (A/Puerto Rico/8/1934(H1N1))

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 9 其他Polymer 6	ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-9WV × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 water × 6	Consistent with protein count
2	Other combination	Heteromer	Protein 9 其他Polymer 6	ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-9WV × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEMA_I34A1
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 18–343 Author chain C； PDBConstruct 1–326； UniProt 18–343 Author chain E； PDBConstruct 1–326； UniProt 18–343 Author chain G； PDBConstruct 1–326； UniProt 18–343 Author chain B； PDBConstruct 1–176； UniProt 344–519 Author chain D； PDBConstruct 1–176； UniProt 344–519 Author chain F； PDBConstruct 1–176； UniProt 344–519 Author chain H； PDBConstruct 1–176； UniProt 344–519

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	5w6r
Deposition date deposition_date	2017-06-16
Structure title title	Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)
Keywords keywords	Glycoprotein, Ectodomain, N-glycosylation, VIRAL PROTEIN, VIRAL PROTEIN-PEPTIDE complex; VIRAL PROTEIN/PEPTIDE
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.

5w6r__assembly_2__model_1

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

Download this curve (.dat)

5w6r__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w6r__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	42.46 Å
Rg (electron density)	41.87 Å
Total Rg	42.00 Å
Atom count	12396
Residues	1503
Excluded volume	218940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w6r__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5w6r__assembly_2__model_1`	nonameric （9）	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 (6)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	36650.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	16630

DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIAGWLLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFPKESSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGIHHPPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDTIIFEANGNLIAPMYAFALSRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSR

Source Source

Source organism organism	Influenza A virus (A/Puerto Rico/8/1934(H1N1))
NCBI taxonomy ID ncbi_taxonomy_id	211044
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	20138.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNTVIEKMNIQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYPKYSEESKLNREKVDGV

Source Source

Source organism organism	Influenza A virus (A/Puerto Rico/8/1934(H1N1))
NCBI taxonomy ID ncbi_taxonomy_id	211044
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-9WV
Molecular weight formula_weight	1558.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,O,N,Q

XXALEYFEWLSX

Entity 4 Entity 4 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	8

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	12

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5w6rA01
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	5w6rA02
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	5w6rB00
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	5w6rC01
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	5w6rC02
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	5w6rD00
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	5w6rE01
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	5w6rE02
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	5w6rF00
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	5w6rG01
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	5w6rG02
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	5w6rH00
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	234.461 Å
Unit-cell length b length_b	234.461 Å
Unit-cell length c length_c	144.560 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	36

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.731 Å
Low-resolution limit resolution_low	44.338 Å
R factor r_factor	0.2001
R_work r_work	0.1981
R_free r_free	0.2392

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)

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

Hemagglutinin

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

5w6r__assembly_2__model_1

5w6r__assembly_2__model_1 | I(q)

5w6r__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)

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

Hemagglutinin

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

5w6r__assembly_2__model_1

5w6r__assembly_2__model_1 | I(q)

5w6r__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)