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9y40

Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 49_C09 antibody

Method: X-RAY DIFFRACTION D_max: 120.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y40
deposition_date	2025-09-02
title	Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 49_C09 antibody
keywords	Hemagglutinin, Head antibody, Influenza, Complex, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	34.53 Å
rg_electron	34.69 Å
i0	93449300.00
molecular_weight	75970.0 kDa
excluded_volume	94544 Å³
envelope_volume	122700 Å³
shell_volume	32290 Å³
envelope_diameter	129.2 Å
shell_rg	37.33 Å
envelope_rg	35.22 Å
shape_rg	34.64 Å
total_rg	35.07 Å
total_atoms	5348
n_residues	684
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	120.0 Å
rg_real	34.91 Å
rg_real_error	1.31 Å
i0_real	9.3450e+07
i0_real_error	1.7030e+06
rg_reciprocal	34.68 Å
i0_reciprocal	93430000.0000
total_estimate	0.8226
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.3 Å
skewness	0.590
kurtosis	-0.247
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	11840000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.724; Smooth: 0.819

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Hemagglutinin
formula_weight	29946.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5356

VQSSSTGRICDSPHRILDGKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFTNEGFNWTGVAQDGTSYACKRGSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIWGVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRITYGACPRYVK

Source

organism	Influenza A virus (A/New York/631/1996(H3N2))
ncbi_taxonomy_id	375621
host_organism	Trichoplusia ni

Entity 2 polymer

description	Antibody 49_C09 heavy chain
formula_weight	24094.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QSTLKESGPTLVKPTETLTLTCTFSGFSLHTSGVGVGWIRQPPGKALECLALIYWNDDARYSPSLQSRLTITKDTSKNQVVLTMSNMDPVDTATYYCAHKGGGRDGYNSAAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Antibody 49_C09 light chain
formula_weight	22939.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SYVLTQPPSVSVAPGQTARIPCGGNNIGMKTVHWYQQRPGQAPVVVVYDDSRRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSVNHWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	1

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6. Citations (1)

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length_a	170.358 Å
length_b	170.358 Å
length_c	95.831 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	3.710 Å
resolution_low	45.570 Å
r_factor	0.2063
r_work	0.2027
r_free	0.2382

fit	/app/data/saxs_computation/y4/9y40/9y40.fit
pddf	/app/data/pr_computation/y4/9y40/9y40.pr.out
profile	/app/data/saxs_computation/y4/9y40/9y40.dat

Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 49_C09 antibody

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)