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9y3z

Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 3_H2 antibody

Method: X-RAY DIFFRACTION D_max: 123.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y3z
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 3_H2 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	35.52 Å
rg_electron	35.67 Å
i0	98004200.00
molecular_weight	77497.0 kDa
excluded_volume	96262 Å³
envelope_volume	127130 Å³
shell_volume	33023 Å³
envelope_diameter	132.3 Å
shell_rg	37.32 Å
envelope_rg	36.21 Å
shape_rg	35.62 Å
total_rg	35.96 Å
total_atoms	5447
n_residues	689
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	123.9 Å
rg_real	36.00 Å
rg_real_error	1.44 Å
i0_real	9.8000e+07
i0_real_error	1.7130e+06
rg_reciprocal	35.70 Å
i0_reciprocal	97980000.0000
total_estimate	0.7955
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.3 Å
skewness	0.631
kurtosis	-0.188
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	11690000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.621; Smooth: 0.635

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Hemagglutinin
formula_weight	29718.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5931

VQSSSTGRICDSPHRILDGKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFTNEGFNWTGVAQDGTSYACKRGSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIWGVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRITYGACPRY

Source

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

Entity 2 polymer

description	Antibody 3_H2 heavy chain
formula_weight	24185.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QGTLKESGPAMVKPTQTLTLTCTFSGFSLDTSGMCVAWIRQPPGKALEWLALFDWDNNKYYSPSLKTRLNMSKGRSRNQVVLTMTNMDPVDTGTYYCARKVYGSFYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Antibody 3_H2 light chain
formula_weight	23573.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVLTQSPATLSLSPGDSATLSCRASQDVSANLAWYQQKPGQAPRLVIYDATNRATGIPARFSGSGLGTDFTLTISSLEPEDFAVYYCQQRSNWPPVYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

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

Entity 6 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	484

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6. Citations (1)

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length_a	62.767 Å
length_b	123.089 Å
length_c	144.423 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.150 Å
resolution_low	47.370 Å
r_factor	0.1918
r_work	0.1899
r_free	0.2264

fit	/app/data/saxs_computation/y3/9y3z/9y3z.fit
pddf	/app/data/pr_computation/y3/9y3z/9y3z.pr.out
profile	/app/data/saxs_computation/y3/9y3z/9y3z.dat

Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 3_H2 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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)