SAXSdb — 9ub1

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1. Structure Basics

entry_id	9ub1
deposition_date	2025-04-02
title	The structure of Myanmar_N2 and M6B12_Fab complex
keywords	protein, VIRAL PROTEIN/IMMUNE SYSTEM, 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	57.08 Å
rg_electron	57.39 Å
i0	2090040000.00
molecular_weight	370370.0 kDa
excluded_volume	457740 Å³
envelope_volume	697310 Å³
shell_volume	100990 Å³
envelope_diameter	202.3 Å
shell_rg	60.14 Å
envelope_rg	57.37 Å
shape_rg	57.38 Å
total_rg	57.49 Å
total_atoms	26012
n_residues	3312
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	193.5 Å
rg_real	57.10 Å
rg_real_error	2.00 Å
i0_real	2.0900e+09
i0_real_error	4.6230e+07
rg_reciprocal	57.04 Å
i0_reciprocal	2090000000.0000
total_estimate	0.8828
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	69.1 Å
skewness	0.276
kurtosis	-0.488
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	197400000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.797

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Vasodilator-stimulated phosphoprotein,Neuraminidase
formula_weight	54393.0 kDa
ec_number	3.2.1.18
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	26012

MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSEFEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGKGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVVMTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDVWMGRTISEKSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI

Source

organism	Influenza A virus (A/California/VRDL364/2009(mixed))
ncbi_taxonomy_id	1049605
host_organism	Homo sapiens

Entity 2 polymer

description	M6B12 antibody heavy chain
formula_weight	24886.5 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,G,I,K

EVQLVESGGGLVQPGGSLRLSCTVSGFTFTSYEINWVRQAPGKGLEWVSYISQSGSTIYYTDSVQGRFTISRDNAENSVYLQMDSLRVEDTAVYYCARDRLPDRDSGDYESRFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	M6B12 antibody light chain
formula_weight	23523.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	F,H,J,L

DIQMTQSPSSLSASVGDRVTITCQASQDISMHLNWYQQKPGRAPKLLIHGASHLETGGPSRFSGSGSGTDFTFTVSNLQPEDIATYYCQQYFKIPYTFGQGTTLAIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1397.2 kDa
src_method	man
entity_count	4

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	12

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

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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	2.35 Å
resolution_method	—
num_particles	463389

fit	/app/data/saxs_computation/ub/9ub1/9ub1.fit
pddf	/app/data/pr_computation/ub/9ub1/9ub1.pr.out
profile	/app/data/saxs_computation/ub/9ub1/9ub1.dat

The structure of Myanmar_N2 and M6B12_Fab complex

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

EM 3D

5. Entities & Polymer Info (6)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)