5w6g

Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands

Method: X-RAY DIFFRACTION

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

Hemagglutinin HA1

Influenza A virus (A/Solomon Islands/3/2006(H1N1))

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 3	6649 antibody heavy chain × 3 （S6B2B6） 6649 antibody light chain × 3 （Q6GMX4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SULFATE ION × 18 GLYCEROL × 6 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A7UPX0_9INFA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 9–334； UniProt 18–343 Author chain B； PDBConstruct 1–176； UniProt 344–519

6649 antibody heavy chain

Homo sapiens

UniProt S6B2B6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 3	Hemagglutinin HA1 × 3 （A7UPX0） Hemagglutinin HA2 × 3 （A7UPX0） 6649 antibody light chain × 3 （Q6GMX4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SULFATE ION × 18 GLYCEROL × 6 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S6B2B6_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 118–230； UniProt 138–250

6649 antibody light chain

Homo sapiens

UniProt Q6GMX4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 3	Hemagglutinin HA1 × 3 （A7UPX0） Hemagglutinin HA2 × 3 （A7UPX0） 6649 antibody heavy chain × 3 （S6B2B6） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SULFATE ION × 18 GLYCEROL × 6 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6GMX4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain L； PDBConstruct 118–218； UniProt 136–236

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	5w6g
Deposition date deposition_date	2017-06-16
Structure title title	Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
Keywords keywords	Antibody, FAB, Influenza H1N1, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

5w6g__assembly_1__model_1

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

Download this curve (.dat)

5w6g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w6g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	57.32 Å
Rg (electron density)	57.52 Å
Total Rg	57.41 Å
Atom count	22008
Residues	2799
Excluded volume	387840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w6g__assembly_1__model_1`	dodecameric （12）	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 (9)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1
Molecular weight formula_weight	37239.7 kDa
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	7347

ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSR

Source Source

Source organism organism	Influenza A virus (A/Solomon Islands/3/2006(H1N1))
NCBI taxonomy ID ncbi_taxonomy_id	464623
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2
Molecular weight formula_weight	20356.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKIDGVRS

Source Source

Source organism organism	Influenza A virus (A/Solomon Islands/3/2006(H1N1))
NCBI taxonomy ID ncbi_taxonomy_id	464623
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	6649 antibody heavy chain
Molecular weight formula_weight	24791.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQESGPGLVKTSETLSLTCTVSGGSIKNKDFFWAWIRQPPGKALEWIGSVFYSGGAYYNWSLRNRVTMSADTSKNQFSLKMTSVTASDTSFYYCATSYVDNWHAGLHWFDSWGRGTLVTVSGASTKGPSVFPLAPSSKSTSGGTVALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	6649 antibody light chain
Molecular weight formula_weight	22901.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QSVLTQPPSVSGAPGQRVSISCTGTHSNIGAGFDVHWYQQLPGTAPKLLIYANNNRPSGVPDRFSGSKSGSSASLAITGLQAEDEADYYCQSFDSILSGDLVFGGGTKLTVLGQPKGAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 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 6 Entity 6 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	4

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d5w6ga1
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	d5w6ga2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5w6gb_
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	d5w6gh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5w6gh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5w6gl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5w6gl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	5w6gA01
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	5w6gA02
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	5w6gB00
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	5w6gH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w6gL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w6gL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	177.310 Å
Unit-cell length b length_b	177.310 Å
Unit-cell length c length_c	177.310 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	49.180 Å
R factor r_factor	0.2200
R_work r_work	0.2180
R_free r_free	0.2530

Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands

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

Hemagglutinin HA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

6649 antibody heavy 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

6649 antibody light 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

5w6g__assembly_1__model_1

5w6g__assembly_1__model_1 | I(q)

5w6g__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 (9)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)