SAXSdb — 9fcm

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

;Spike protein S2' ;

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Single-domain antibody R3DC23 × 3 CHLORIDE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 3–55； UniProt 1159–1211 Author chain E； PDBConstruct 3–55； UniProt 1159–1211 Author chain F； PDBConstruct 3–55； UniProt 1159–1211

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	9fcm
Deposition date deposition_date	2024-05-15
Structure title title	Single-domain antibody binding the SARS-COV2 S2
Keywords keywords	single domain anitbodies viral proteins SARS-COV2, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9fcm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9fcm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fcm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.92 Å
Rg (electron density)	28.31 Å
Total Rg	29.01 Å
Atom count	3963
Residues	506
Excluded volume	69662 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fcm__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Single-domain antibody R3DC23
Molecular weight formula_weight	16589.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4266

QVQLQESGGGLVQAGDSLTLSCAVSGRIFSTYTMGWFRQAPGKEREFVAAVRWGAGTIYYADSMKGRFTISRDSAKNTVDLQMNSTKPEDTAVYYCGAAYVSKANYGSLWYQDSRRYDYWGQGTQVTVSSAAAYPYDVPDYGSHHHHHH

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;Spike protein S2' ;
Molecular weight formula_weight	6100.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

GPHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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Unit-cell length a length_a	90.413 Å
Unit-cell length b length_b	98.800 Å
Unit-cell length c length_c	150.763 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	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	82.640 Å
R factor r_factor	0.2021
R_work r_work	0.1997
R_free r_free	0.2467

Single-domain antibody binding the SARS-COV2 S2

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

;Spike protein S2' ;

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9fcm__assembly_1__model_1

9fcm__assembly_1__model_1 | I(q)

9fcm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Single-domain antibody binding the SARS-COV2 S2

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

;Spike protein S2' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9fcm__assembly_1__model_1

9fcm__assembly_1__model_1 | I(q)

9fcm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)