← Back to search

9utf

Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex XG83 Fab

Method: X-RAY DIFFRACTION D_max: 102.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9utf
deposition_date	2025-05-03
last_revision	2026-05-06
title	Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex XG83 Fab
keywords	antibody complex, Neutralization, ANTIVIRAL PROTEIN, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.95 Å
rg_electron	30.74 Å
i0	73948200.00
molecular_weight	67179.0 kDa
excluded_volume	83790 Å³
envelope_volume	111930 Å³
shell_volume	31936 Å³
envelope_diameter	106.3 Å
shell_rg	36.19 Å
envelope_rg	30.58 Å
shape_rg	30.72 Å
total_rg	31.33 Å
total_atoms	4735
n_residues	627
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

▼

3. P(r) Analysis (GNOM)

dmax	102.2 Å
rg_real	31.12 Å
rg_real_error	0.89 Å
i0_real	7.3950e+07
i0_real_error	1.2200e+06
rg_reciprocal	31.05 Å
i0_reciprocal	73940000.0000
total_estimate	0.8680
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.1 Å
skewness	0.452
kurtosis	-0.457
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	10510000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.864; Smooth: 0.876

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	XG83 antibody
formula_weight	25057.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	4735

MAWSPLLLTLLAHCTGSWAQSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGDSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADFYCQSYDSSLSTSIFGGGTKLTVLRTGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Spike protein S1
formula_weight	30338.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCS

Source

organism	Severe acute respiratory syndrome coronavirus
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 3 polymer

description	XG83 antibody
formula_weight	27759.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MDWTWRFLFVVAAATGVQSQVQLVQSGAEVKKPGSSVKVSCKASGDTFSSYTITWVRQAPGQGLEWMGRVIPILGTANYAQKFQGRVTITADKSTRTAYMELSSLRSDDSAMYYCARERGYSGNGAAYYFDYWGQGTLVTVSSKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGG

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 non-polymer

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

▶

6. Citations (1)

▶

length_a	60.044 Å
length_b	194.411 Å
length_c	151.723 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

resolution	2.950 Å
resolution_low	44.870 Å
r_factor	0.2542
r_work	0.2520
r_free	0.2949

fit	/app/data/saxs_computation/ut/9utf/9utf.fit
pddf	/app/data/pr_computation/ut/9utf/9utf.pr.out
profile	/app/data/saxs_computation/ut/9utf/9utf.dat

Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex XG83 Fab

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)