6j10

Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly

Method: X-RAY DIFFRACTION

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

Capsid protein

Hepatitis B virus genotype D subtype adw

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one × 3 water × 6	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149 Author chain C； PDBConstruct 1–149； UniProt 1–149 Author chain D； PDBConstruct 1–149； UniProt 1–149 Author chain E； PDBConstruct 1–149； UniProt 1–149 Author chain F； 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	6j10
Deposition date deposition_date	2018-12-27
Structure title title	Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly
Keywords keywords	Hepatitis B virus, Ciclopirox, Capsid assembly inhibitor, VIRAL PROTEIN; VIRAL 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.

6j10__assembly_1__model_1

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

Download this curve (.dat)

6j10__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6j10__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.42 Å
Rg (electron density)	32.66 Å
Total Rg	33.27 Å
Atom count	6654
Residues	846
Excluded volume	119290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6j10__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 (3)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	16692.1 kDa
Mutation mutation	Y132A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6946

MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVV

Source Source

Source organism organism	Hepatitis B virus genotype D subtype adw
Common name common_name	HBV
NCBI taxonomy ID ncbi_taxonomy_id	10419
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one
Molecular weight formula_weight	207.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	292

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6j10a_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d6j10b_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d6j10c_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d6j10d_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d6j10e_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d6j10f_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

CATH v4.4 (6 domains)

Domain ID domain_id	6j10A00
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	6j10B00
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	6j10C00
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	6j10D00
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	6j10E00
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	6j10F00
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	153.924 Å
Unit-cell length b length_b	88.510 Å
Unit-cell length c length_c	99.162 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.700 Å
R factor r_factor	0.2597
R_work r_work	0.2575
R_free r_free	0.3035

Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly

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

6j10__assembly_1__model_1

6j10__assembly_1__model_1 | I(q)

6j10__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly

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

6j10__assembly_1__model_1

6j10__assembly_1__model_1 | I(q)

6j10__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)