SAXSdb — 9bdf

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

Hemagglutinin

Influenza A virus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 9 其他Polymer 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 17–521 Chain G； UniProt 17–521 Chain H； UniProt 17–521	Not recorded	ADI-85666 Fab heavy chain × 3 ADI-85666 Fab light chain × 3 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.01 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9BDF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11MS Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 0.25x SurfACT Deposited 2026-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–521（521 aa） Chain B 1–521（521 aa） Chain C 1–521（521 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 2.39 Å
11MT Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry) determined using the SPT Labtech chameleon in the presence of 0.25x SurfACT Deposited 2026-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–521（521 aa） Chain B 1–521（521 aa） Chain C 1–521（521 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 2.16 Å
11MU Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT Deposited 2026-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–521（521 aa） Chain B 1–521（521 aa） Chain C 1–521（521 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 2.67 Å
11MV Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT Deposited 2026-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–521（521 aa） Chain B 1–521（521 aa） Chain C 1–521（521 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 2.47 Å
9BDG Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647 Deposited 2024-04-11	Different oligomeric state Different ligand/ion	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 17–521（505 aa） Chain B 17–521（505 aa） Chain C 17–521（505 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8F5JT24_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–505； UniProt 17–521 Author chain G； PDBConstruct 1–505； UniProt 17–521 Author chain H； PDBConstruct 1–505； UniProt 17–521

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	9bdf
Deposition date deposition_date	2024-04-11
Structure title title	Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85666
Keywords keywords	Hemagglutinin, Influenza A, Antibody, Fab, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	49.11 Å
Radius of gyration Rg (electron density) rg_electron	48.72 Å
Forward intensity I(0) i0	914558000.00
Molecular weight molecular_weight	244220.0 kDa
Excluded volume excluded_volume	302740 Å³
Envelope volume envelope_volume	437840 Å³
Hydration-shell volume shell_volume	75272 Å³
Envelope diameter envelope_diameter	146.6 Å
Shell Rg shell_rg	52.45 Å
Envelope Rg envelope_rg	47.78 Å
Shape Rg shape_rg	48.71 Å
Total Rg total_rg	48.90 Å
Total atoms total_atoms	17167
Residues n_residues	2126
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	149.9 Å
Rg (real space) rg_real	48.94 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	9.1460e+08
I(0) uncertainty (real space) i0_real_error	1.5440e+07
Rg (reciprocal space) rg_reciprocal	49.11 Å
I(0) (reciprocal space) i0_reciprocal	914700000.0000
Solution quality estimate total_estimate	0.8921
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.5 Å
Skewness Skewness skewness	0.111
Kurtosis Kurtosis kurtosis	-0.811
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	59950000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.670

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	57485.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,H
Atom count atom_count	17167

QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICGSPHQILDGGNCTLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSSSSFFSRLNWLTSLNNIYPAQNVTMPNKEQFDKLYIWGVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRWQNSEGRGQAADLKSTQAAIDQINGILNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALINQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGAGSSLEVLFQ

来源 Source

来源生物 organism	Influenza A virus
NCBI Class编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	ADI-85666 Fab heavy chain
Molecular weight formula_weight	25579.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,E

EVQLLESGPGLVKPSETLSLTCSLSGGFVTRNSYYLSWVRQPPGKGMEWIGYVHHSGETKYNPSLKSRVTMSMDASKNQFSLRLRSVTAADTAVYYCARDLVEGGYIPFSYGLDVWGLGTTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSSLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	ADI-85666 Fab light chain
Molecular weight formula_weight	23403.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I,J

DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPERLIYAASSSLPGVPSRFRGSGSGTEFTLTISSLQPEDSATYFCLQYHNYPRTFGPGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-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	748.7 kDa
Source method src_method	man
Copy count entity_count	3

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	5

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	16

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.01 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	315433

fit	/app/data/saxs_computation/bd/9bdf/9bdf.fit
pddf	/app/data/pr_computation/bd/9bdf/9bdf.pr.out
profile	/app/data/saxs_computation/bd/9bdf/9bdf.dat

Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85666

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)