SAXSdb — 9z80

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1. Structure Basics

entry_id	9z80
deposition_date	2025-11-18
title	SARS-CoV-2 S2 in complex with polyclonal Fab_Donor1
keywords	SARS-CoV-2, Coronavirus, Immune system, antibody, 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	37.89 Å
rg_electron	36.97 Å
i0	369826000.00
molecular_weight	154340.0 kDa
excluded_volume	192280 Å³
envelope_volume	258380 Å³
shell_volume	57350 Å³
envelope_diameter	139.4 Å
shell_rg	43.50 Å
envelope_rg	37.37 Å
shape_rg	37.03 Å
total_rg	37.21 Å
total_atoms	10854
n_residues	1443
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	130.6 Å
rg_real	37.96 Å
rg_real_error	1.22 Å
i0_real	3.6980e+08
i0_real_error	6.4840e+06
rg_reciprocal	37.92 Å
i0_reciprocal	369800000.0000
total_estimate	0.8698
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.5 Å
skewness	0.419
kurtosis	-0.268
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	97890000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.956

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Human polyclonal Fab model with polyalanine backbone - Heavy chain
formula_weight	10118.6 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	10854

XXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXXXXXXX

Entity 2 polymer

description	Human polyclonal Fab model with polyalanine backbone - Light chain
formula_weight	7905.9 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

XXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXX

Entity 3 polymer

description	Spike protein S2
formula_weight	52342.1 kDa
mutation	S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,D,E

SLGAENCVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLACTITSGWTCGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNFLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSGSHHHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 4 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	7

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	5

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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	triclinic

resolution	3.17 Å
resolution_method	—
num_particles	35264

fit	/app/data/saxs_computation/z8/9z80/9z80.fit
pddf	/app/data/pr_computation/z8/9z80/9z80.pr.out
profile	/app/data/saxs_computation/z8/9z80/9z80.dat

SARS-CoV-2 S2 in complex with polyclonal Fab_Donor1

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)