SAXSdb — 9vdz

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1. Structure Basics

entry_id	9vdz
deposition_date	2025-06-09
title	hA5-6(W30B/E45) Fab bound to SFTSV glycoprotein Gn
keywords	glycoprotein, Gn, Fab, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	43.50 Å
rg_electron	43.19 Å
i0	409222000.00
molecular_weight	162680.0 kDa
excluded_volume	201890 Å³
envelope_volume	283880 Å³
shell_volume	54560 Å³
envelope_diameter	143.5 Å
shell_rg	48.74 Å
envelope_rg	41.95 Å
shape_rg	43.15 Å
total_rg	43.60 Å
total_atoms	11419
n_residues	1464
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	144.5 Å
rg_real	43.42 Å
rg_real_error	1.61 Å
i0_real	4.0920e+08
i0_real_error	7.8060e+06
rg_reciprocal	43.50 Å
i0_reciprocal	409300000.0000
total_estimate	0.8243
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	60.2 Å
skewness	0.147
kurtosis	-0.601
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	24660000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	hA5-6(W30B/E45) Fab heavy chain
formula_weight	25016.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,H
atom_count	11704

QVQLVQSGPELKKPGASVKVSCKASGYSFSDDWMYWVRQSPGKGLEWIGRIDPDNGGTSYAQKFKGRVTLTVDKSSSTAFMELNSLTSEDTAVYYCAREDYYGSRAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	hA5-6(W30B/E45) Fab light chain
formula_weight	23794.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,L

DIVLTQSPASLAVSLGERATISCKASQSVDYWGDSYMNWYQQKPGQPPELLIYAASNLESGVPDRFSGSGSGTDFTLTISSVQAEDVAVYYCQQSYEDPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Envelopment polyprotein
formula_weight	37412.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

DTGPIICAGPIHSNKSADIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKGSDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSRTSSGLLPSDRVLWIGDVACQPMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKTCKTSGSCRGDMQFCKVAGCEHGEEASEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLEVSGSTLEVLFQGPHHHHHH

Source

organism	Severe fever with thrombocytopenia syndrome virus
ncbi_taxonomy_id	1003835
host_organism	Trichoplusia ni

Entity 4 branched

description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	285

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6. Citations (1)

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length_a	65.200 Å
length_b	91.360 Å
length_c	309.800 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	2.430 Å
resolution_low	29.880 Å
r_factor	0.2043
r_work	0.2016
r_free	0.2555

fit	/app/data/saxs_computation/vd/9vdz/9vdz.fit
pddf	/app/data/pr_computation/vd/9vdz/9vdz.pr.out
profile	/app/data/saxs_computation/vd/9vdz/9vdz.dat

hA5-6(W30B/E45) Fab bound to SFTSV glycoprotein Gn

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)