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9rcu

Cardioderma bat coronavirus 2B receptor binding domain in complex with human CEACAM6

Method: X-RAY DIFFRACTION D_max: 158.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rcu
deposition_date	2025-05-29
title	Cardioderma bat coronavirus 2B receptor binding domain in complex with human CEACAM6
keywords	RECEPTOR, RECEPTOR BINDING DOMAIN, VIRUS ENTRY, VIRUS:HOST INTERACTION, VIRAL PROTEIN; VIRAL PROTEIN
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	42.93 Å
rg_electron	44.59 Å
i0	34344000.00
molecular_weight	46482.0 kDa
excluded_volume	57950 Å³
envelope_volume	87156 Å³
shell_volume	20337 Å³
envelope_diameter	161.0 Å
shell_rg	37.48 Å
envelope_rg	45.20 Å
shape_rg	44.53 Å
total_rg	44.28 Å
total_atoms	3275
n_residues	401
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	158.4 Å
rg_real	44.03 Å
rg_real_error	2.40 Å
i0_real	3.4340e+07
i0_real_error	6.3090e+05
rg_reciprocal	42.94 Å
i0_reciprocal	34300000.0000
total_estimate	0.5826
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	21.4 Å
skewness	0.664
kurtosis	-0.381
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	1022000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.080; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.031; Smooth: 0.300

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cell adhesion molecule CEACAM6
formula_weight	32685.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3275

KLTIESTPFNVAEGKEVLLLAHNLPQNRIGYSWYKGERVDGNSLIVGYVIGTQQATPGPAYSGRETIYPNASLLIQNVTQNDTGFYTLQVIKSDLVNEEATGQFHVYPELPKPSISSNNSNPVEDKDAVAFTCEPEVQNTTYLWWVNGQSLPVSPRLQLSNGNMTLTLLSVKRNDAGSYECEIQNPASANRSDPVTLNVLYGPDVPTISPSKANYRPGENLNLSCHAASNPPAQYSWFINGTFQQSTQELFIPNITVNNSGSYMCQAHNSATGLNRTTVTMITVSGSAPVLSKLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Spike protein
formula_weight	16879.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

VALPYHATHSFVNFTVWRGSTDNGSFVYINGGPEPFCVNTTQFTTNFEQLNKTFTSIEAKLQGGDCPFTLASLNNYLSFDSICFSVQPVGASCTLSIQIGWMGYFIPWRDIYVTFKHGSTITGVTKAATGNDIFEAQKIEWHEKHHHHHH

Source

organism	Cardioderma bat coronavirus
ncbi_taxonomy_id	3119326
host_organism	Homo sapiens

Entity 3 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	2

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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length_a	47.553 Å
length_b	76.856 Å
length_c	204.975 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.990 Å
resolution_low	61.490 Å
r_factor	0.2550
r_work	0.2528
r_free	0.2973

fit	/app/data/saxs_computation/rc/9rcu/9rcu.fit
pddf	/app/data/pr_computation/rc/9rcu/9rcu.pr.out
profile	/app/data/saxs_computation/rc/9rcu/9rcu.dat

Cardioderma bat coronavirus 2B receptor binding domain in complex with human CEACAM6

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 branched

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)