SAXSdb — 9vdy

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1. Structure Basics

entry_id	9vdy
deposition_date	2025-06-09
title	hA5-6 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	43.00 Å
rg_electron	42.95 Å
i0	408156000.00
molecular_weight	161530.0 kDa
excluded_volume	200450 Å³
envelope_volume	278630 Å³
shell_volume	55704 Å³
envelope_diameter	155.5 Å
shell_rg	46.27 Å
envelope_rg	42.12 Å
shape_rg	42.90 Å
total_rg	43.25 Å
total_atoms	11338
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	146.2 Å
rg_real	43.10 Å
rg_real_error	1.39 Å
i0_real	4.0820e+08
i0_real_error	6.9900e+06
rg_reciprocal	43.00 Å
i0_reciprocal	408100000.0000
total_estimate	0.8644
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.4 Å
skewness	0.394
kurtosis	-0.136
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	26980000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.677

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Envelopment polyprotein
formula_weight	37412.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11591

DTGPIICAGPIHSNKSADIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKGSDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSRTSSGLLPSDRVLWIGDVACQPMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKTCKTSGSCRGDMQFCKVAGCEHGEEASEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLEVSGSTLEVLFQGPHHHHHH

Source

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

Entity 2 polymer

description	hA5-6 Fab heavy chain
formula_weight	25016.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,H

QVQLVQSGPELKKPGASVKVSCKASGYSFSDDWMYWVRQSPGKGLEWIGRIDPDNGGTSYAQKFKGRVTLTVDKSSSTAFMELNSLTSEDTAVYYCAREDYYGSRAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	hA5-6 Fab light chain
formula_weight	23679.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,L

DIVLTQSPASLAVSLGERATISCKASQSVDYAGDSYMNWYQQKPGQPPKLLIYAASNLESGVPDRFSGSGSGTDFTLTISSVQAEDVAVYYCQQSYEDPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	253

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6. Citations (1)

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length_a	64.960 Å
length_b	91.110 Å
length_c	308.270 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	2.280 Å
resolution_low	29.930 Å
r_factor	0.2059
r_work	0.2040
r_free	0.2401

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

hA5-6 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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)