SAXSdb — 9zt7

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1. Structure Basics

entry_id	9zt7
deposition_date	2025-12-23
title	SARS-CoV-2 S2 in complex with COV2-2509
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	44.55 Å
rg_electron	44.40 Å
i0	523602000.00
molecular_weight	188470.0 kDa
excluded_volume	235890 Å³
envelope_volume	325790 Å³
shell_volume	62544 Å³
envelope_diameter	155.2 Å
shell_rg	47.50 Å
envelope_rg	44.66 Å
shape_rg	44.40 Å
total_rg	44.56 Å
total_atoms	13245
n_residues	1665
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	154.9 Å
rg_real	44.82 Å
rg_real_error	1.67 Å
i0_real	5.2360e+08
i0_real_error	1.0090e+07
rg_reciprocal	44.56 Å
i0_reciprocal	523400000.0000
total_estimate	0.8365
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.2 Å
skewness	0.473
kurtosis	-0.409
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	70970000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.778

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	COV2-2509 Fab-Heavy chain
formula_weight	23965.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	13245

QVQLVESGGGVVQPGRSLRLSCAASGFIFSTYAMHWVRQAPGKGLEWVAVISYDGDNKYYADSVKGRFTISRDNSKNTLYLEMNSLRAEDTAVYYCARPRGGSYQTCFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	COV2-2509 Fab-Light chain
formula_weight	23285.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPGTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
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	10

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 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	triclinic

resolution	3.11 Å
resolution_method	—
num_particles	139283

fit	/app/data/saxs_computation/zt/9zt7/9zt7.fit
pddf	/app/data/pr_computation/zt/9zt7/9zt7.pr.out
profile	/app/data/saxs_computation/zt/9zt7/9zt7.dat

SARS-CoV-2 S2 in complex with COV2-2509

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)