SAXSdb — 9x5y

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1. Structure Basics

entry_id	9x5y
deposition_date	2025-10-14
title	B/Brisbane/60/2008 HA in complex with BO-6B
keywords	Hemagglutinin, HA, antibody, influenza B virus, BO-6B, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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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	44.88 Å
rg_electron	44.64 Å
i0	774094000.00
molecular_weight	225860.0 kDa
excluded_volume	281380 Å³
envelope_volume	384050 Å³
shell_volume	71362 Å³
envelope_diameter	141.3 Å
shell_rg	48.36 Å
envelope_rg	45.35 Å
shape_rg	44.64 Å
total_rg	44.80 Å
total_atoms	15870
n_residues	1995
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	141.3 Å
rg_real	44.71 Å
rg_real_error	1.36 Å
i0_real	7.7410e+08
i0_real_error	1.5070e+07
rg_reciprocal	44.88 Å
i0_reciprocal	774200000.0000
total_estimate	0.9013
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	56.5 Å
skewness	0.119
kurtosis	-0.690
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	124600000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.859

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Hemagglutinin HA1 chain
formula_weight	39285.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,A,E
atom_count	15930

MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTETRGKLCPKCLNCTDLDVALGRPKCTGKIPSARVSILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEHIRLSTHNVINAENAPGGPYKIGTSGSCPNITNGNGFFATMAWAVPKNDKNKTATNPLTIEVPYICTEGEDQITVWGFHSDNETQMAKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQTEDGGLPQSGRIVVDYMVQKSGKTGTITYQRGILLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLKER

Source

organism	Influenza B virus (B/Brisbane/60/2008)
ncbi_taxonomy_id	604436
host_organism	Cricetulus griseus

Entity 2 polymer

description	Hemagglutinin HA2 chain
formula_weight	25562.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	I,B,F

GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFDAGEFSLPTFDSLNITAASLNDDGLDNHTILDIRSLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

Source

organism	Influenza B virus (B/Brisbane/60/2008)
ncbi_taxonomy_id	604436
host_organism	Cricetulus griseus

Entity 3 polymer

description	BO-6B heavy chain
formula_weight	50954.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	J,C,H

MGWSCIILFLVATATGVHSEVQLVESGGVVVQPGGSLRLSCAASGLNFSNFAMHWVRQAPGKGLEWVSVISWDGGTTFYADSVEGRFTISRDNNKNSLYLEMSSLRPEDTALYYCAQASSWGFFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 polymer

description	BO-6B light chain
formula_weight	25544.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	K,D,L

MGWSCIILFLVATATGVHSEIVLTQSPGTLSLSPGQRATLSCRASQRVDSNYLGWYQQKPGQAPRLLIYGASNRATGIPDRFGGSGSGTDFTLTISRLEPEDIAVYSCQHFGDSWWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 5 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 ;
formula_weight	1073.0 kDa
src_method	man
entity_count	3

Entity 6 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	9

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	9

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.650 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.65 Å
resolution_method	—
num_particles	330198

fit	/app/data/saxs_computation/x5/9x5y/9x5y.fit
pddf	/app/data/pr_computation/x5/9x5y/9x5y.pr.out
profile	/app/data/saxs_computation/x5/9x5y/9x5y.dat

B/Brisbane/60/2008 HA in complex with BO-6B

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)