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9psn

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3

Method: X-RAY DIFFRACTION D_max: 180.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9psn
deposition_date	2025-07-25
title	Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3
keywords	;COVID-19, SARS-CoV-2, Receptor binding domain, Antibody, IMMUNE SYSTEM, IMMUNE SYSTEM-Viral Protein complex, 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	50.73 Å
rg_electron	50.82 Å
i0	789167000.00
molecular_weight	232590.0 kDa
excluded_volume	290570 Å³
envelope_volume	420780 Å³
shell_volume	71739 Å³
envelope_diameter	175.4 Å
shell_rg	51.81 Å
envelope_rg	49.96 Å
shape_rg	50.78 Å
total_rg	50.99 Å
total_atoms	16378
n_residues	2085
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	180.9 Å
rg_real	50.83 Å
rg_real_error	2.14 Å
i0_real	7.8920e+08
i0_real_error	1.5850e+07
rg_reciprocal	50.64 Å
i0_reciprocal	789000000.0000
total_estimate	0.8640
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.2 Å
skewness	0.371
kurtosis	-0.313
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	47970000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.885

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	Spike protein S1 receptor binding domain
formula_weight	23520.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,T
atom_count	17097

TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLSGHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	CC12.3 Fab heavy chain
formula_weight	23377.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,M

QVQLVESGGGLIQPGGSLRLSCAASGFTVSSNYMSWVRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSKSTLYLQMNSLRVEDTAVYYCARDFGDFYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	CC12.3 Fab light chain
formula_weight	23432.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,N

EIVLTQSPGTLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	BoWLB-105 Fab heavy chain
formula_weight	23313.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	O,Q

EVQLVQSGAEVKKPGESLKISCKGSGYTFITYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSINTAYLQWSSLTASDTAIYYCAGSSGSSTPMDVWGQGTTVTVSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 5 polymer

description	BoWLB-105 Fab light chain
formula_weight	24430.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	P,R

DIVMSQSPSSLTVSVGERVSMSCKSSQSLLYSTIQKNYLAWYQQKPGQSPKLLIYWASSRESGVPDRFTGSESGTDFTLTISSVKAEDLAVYYCQQYHSYPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 6 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	1

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 9 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	8

Entity 10 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	nat
entity_count	4

Entity 11 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 12 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	697

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6. Citations (1)

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length_a	55.130 Å
length_b	100.855 Å
length_c	127.536 Å
angle_alpha	87.92 °
angle_beta	79.18 °
angle_gamma	89.89 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.540 Å
resolution_low	42.020 Å
r_factor	0.2030
r_work	0.2017
r_free	0.2543

fit	/app/data/saxs_computation/ps/9psn/9psn.fit
pddf	/app/data/pr_computation/ps/9psn/9psn.pr.out
profile	/app/data/saxs_computation/ps/9psn/9psn.dat

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3

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 (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 branched

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)