SAXSdb — 6cwd

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

Capsid protein

Hepatitis B virus subtype adyw

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Single chain variable fragment (scFv) e13 × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Single chain variable fragment (scFv) e13 × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAPSD_HBVD1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–149； UniProt 1–149 Author chain D； PDBConstruct 1–149； UniProt 1–149 Author chain F； PDBConstruct 1–149； UniProt 1–149 Author chain H； PDBConstruct 1–149； UniProt 1–149

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	6cwd
Deposition date deposition_date	2018-03-30
Structure title title	Hepatitis B core-antigen in complex with scFv e13
Keywords keywords	core-antigen, nucleocapsid, scFv, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

6cwd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6cwd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cwd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	34.93 Å
Rg (electron density)	34.93 Å
Total Rg	35.33 Å
Atom count	5397
Residues	716
Excluded volume	96277 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cwd__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6cwd__assembly_2__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	Single chain variable fragment (scFv) e13
Molecular weight formula_weight	26810.7 kDa
Mutation mutation	C48A, C147A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G,A,E
Atom count atom_count	10852

AAELVLTQTPSSVSAAVGGTVTINCQASQSISSRLGWYQQKPGQPPKLLIYGASTLTSVGPSRFKGSGSGTEFTLTISGVQRDDAATYYCLGSDTSTDTAFGGGTEVVVKGGSSRSSSSGGGGSGGGGQEQLVESGGRLVPPGGSLTLTCTVSGIDLSSNAISWVRQAPGKGLEYIGIIYGGSIPYYSRWAKGRFTISKTSTTVALKMSTLTASDTATYFCARGKSDGDGYAAYRLDPWGLGTLVTISSLVPRGSHHHHHH

Source Source

Source organism organism	Oryctolagus cuniculus
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Capsid protein
Molecular weight formula_weight	16720.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETTVV

Source Source

Source organism organism	Hepatitis B virus subtype adyw
NCBI taxonomy ID ncbi_taxonomy_id	10419
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6cwdC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	6cwdD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	6cwdF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	6cwdH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

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Unit-cell length a length_a	219.540 Å
Unit-cell length b length_b	65.100 Å
Unit-cell length c length_c	148.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.330 Å
Low-resolution limit resolution_low	19.918 Å
R factor r_factor	0.2451
R_work r_work	0.2424
R_free r_free	0.2821

Hepatitis B core-antigen in complex with scFv e13

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

Capsid protein

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

6cwd__assembly_2__model_1

6cwd__assembly_2__model_1 | I(q)

6cwd__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Hepatitis B core-antigen in complex with scFv e13

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

Capsid protein

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

6cwd__assembly_2__model_1

6cwd__assembly_2__model_1 | I(q)

6cwd__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)