SAXSdb — 9ssm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain R； UniProt 318–538	Not recorded	084-7D Fab Heavy Chain × 1 084-7D Fab Light Chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；8.25% PEG 3350 4.95% MPD 0.2 M Lithium sulfate 0.1 M imidazole/hydrochloric acid pH 6.5 20% Ethylene glycol added after crystallization	Resolution 2.70 Å R-free 0.269

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9SSM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8QH1 Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194 Deposited 2023-09-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 328–527（200 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M sodium malonate	Resolution 2.65 Å R-free 0.232

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8A5XRG7_SARS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain R； PDBConstruct 1–221； UniProt 318–538

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ssm
Deposition date deposition_date	2025-09-26
Structure title title	Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD
Keywords keywords	Neutralizing antibody SARS-CoV-2 Beta variant, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.84 Å
Radius of gyration Rg (electron density) rg_electron	31.81 Å
Forward intensity I(0) i0	72138100.00
Molecular weight molecular_weight	65917.0 kDa
Excluded volume excluded_volume	81705 Å³
Envelope volume envelope_volume	106110 Å³
Hydration-shell volume shell_volume	30278 Å³
Envelope diameter envelope_diameter	114.6 Å
Shell Rg shell_rg	35.74 Å
Envelope Rg envelope_rg	31.90 Å
Shape Rg shape_rg	31.77 Å
Total Rg total_rg	32.26 Å
Total atoms total_atoms	8948
Residues n_residues	619
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	111.7 Å
Rg (real space) rg_real	32.24 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	7.2140e+07
I(0) uncertainty (real space) i0_real_error	1.2620e+06
Rg (reciprocal space) rg_reciprocal	32.07 Å
I(0) (reciprocal space) i0_reciprocal	72130000.0000
Solution quality estimate total_estimate	0.8194
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.604
Kurtosis Kurtosis kurtosis	-0.151
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11010000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.694

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	084-7D Fab Heavy Chain
Molecular weight formula_weight	24397.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	9014

EVQLLESGGGLVQPGGSLRLSCAASGFSFSSYAMNWVRQAPGKGLEWVSAISGGGDNIYYADSVKGRFTISRDNYKNTLHLQMKSLRAEDTAVYYCAKDHPSWGSSFLNWGQGILVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	084-7D Fab Light Chain
Molecular weight formula_weight	23401.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGRAPKLLIYTASNLESGVPSRFSGSGSGTEFSLTISSLQPDDFATYYCQQYNSYSLTFGGGTRVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	28143.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGGPGHHHHHHHHGGLNDIFEAQKIEWHE

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI Class编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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8. Citations (1)

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Unit-cell length a length_a	81.450 Å
Unit-cell length b length_b	84.368 Å
Unit-cell length c length_c	126.239 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2249
R_work r_work	0.2226
R_free r_free	0.2690

fit	/app/data/saxs_computation/ss/9ssm/9ssm.fit
pddf	/app/data/pr_computation/ss/9ssm/9ssm.pr.out
profile	/app/data/saxs_computation/ss/9ssm/9ssm.dat

Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)