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9xeg

Structure of the Mid-Cap-627 linker domains of the H5N1 influenza A PB2 subunit in complex with onradivir

Method: X-RAY DIFFRACTION D_max: 69.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xeg
deposition_date	2025-10-28
last_revision	2026-06-03
title	Structure of the Mid-Cap-627 linker domains of the H5N1 influenza A PB2 subunit in complex with onradivir
keywords	Influenza virus polymerase, VIRUS, VIRAL PROTEIN; VIRAL 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	20.86 Å
rg_electron	19.87 Å
i0	19651500.00
molecular_weight	32621.0 kDa
excluded_volume	40502 Å³
envelope_volume	48012 Å³
shell_volume	20370 Å³
envelope_diameter	68.5 Å
shell_rg	26.04 Å
envelope_rg	19.96 Å
shape_rg	19.89 Å
total_rg	20.66 Å
total_atoms	4577
n_residues	286
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	69.4 Å
rg_real	20.80 Å
rg_real_error	0.34 Å
i0_real	1.9650e+07
i0_real_error	2.4080e+05
rg_reciprocal	20.81 Å
i0_reciprocal	19650000.0000
total_estimate	0.8874
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.273
kurtosis	-0.396
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0001
highest_alpha	6053000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Polymerase basic protein 2
formula_weight	32511.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5067

GGEVRNDDVDQSLIIAARNIVRRATVSTDPLASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTERLTITYSSSMM

Source

organism	Influenza A virus (strain A/Silky Chicken/Hong Kong/YU100/2002 H5N1 genotype X3)
ncbi_taxonomy_id	284214
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;(2~{S},3~{S})-3-[[6-cyclopropyl-5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid ;
formula_weight	440.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	392

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6. Citations (1)

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length_a	40.559 Å
length_b	59.377 Å
length_c	53.953 Å
angle_alpha	90.00 °
angle_beta	107.57 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.450 Å
resolution_low	51.440 Å
r_factor	0.1237
r_work	0.1210
r_free	0.1730

fit	/app/data/saxs_computation/xe/9xeg/9xeg.fit
pddf	/app/data/pr_computation/xe/9xeg/9xeg.pr.out
profile	/app/data/saxs_computation/xe/9xeg/9xeg.dat

Structure of the Mid-Cap-627 linker domains of the H5N1 influenza A PB2 subunit in complex with onradivir

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