3kxs

Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw

Method: X-RAY DIFFRACTION

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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 homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–143； UniProt 1–143 Author chain B； PDBConstruct 1–143； UniProt 1–143 Author chain C； PDBConstruct 1–143； UniProt 1–143 Author chain D； PDBConstruct 1–143； UniProt 1–143 Author chain E； PDBConstruct 1–143； UniProt 1–143 Author chain F； PDBConstruct 1–143； UniProt 1–143

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	3kxs
Deposition date deposition_date	2009-12-03
Structure title title	Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw
Keywords keywords	;Core protein, capsid, hepadnavirus, four helix bundle, icosahedral, dimer, Capsid protein, DNA-binding, Host cytoplasm, Host-virus interaction, Phosphoprotein, RNA-binding, Virion, 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.

3kxs__assembly_1__model_1

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

Download this curve (.dat)

3kxs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kxs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.83 Å
Rg (electron density)	21.06 Å
Total Rg	21.80 Å
Atom count	2259
Residues	285
Excluded volume	40447 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kxs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3kxs__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3kxs__assembly_3__model_1`	dimeric （2）	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)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3kxsa_
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	d3kxsb_
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	d3kxsc_
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	d3kxsd_
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	d3kxse_
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	d3kxsf_
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	3kxsA00
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	3kxsB00
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	3kxsC00
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	3kxsD00
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	3kxsE00
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	3kxsF00
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	104.162 Å
Unit-cell length b length_b	104.162 Å
Unit-cell length c length_c	86.917 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	25.320 Å
R factor r_factor	0.2197
R_work r_work	0.2172
R_free r_free	0.2642

Description description	Capsid protein
Molecular weight formula_weight	16065.4 kDa
Mutation mutation	Y132A
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,E,C,D,A,B
Atom count atom_count	6932

Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw

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

3kxs__assembly_1__model_1

3kxs__assembly_1__model_1 | I(q)

3kxs__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw

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

3kxs__assembly_1__model_1

3kxs__assembly_1__model_1 | I(q)

3kxs__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)