5e0i

Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution

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	methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate × 6 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 2–150； UniProt 1–149 Author chain B； PDBConstruct 2–150； UniProt 1–149 Author chain C； PDBConstruct 2–150； UniProt 1–149 Author chain D； PDBConstruct 2–150； UniProt 1–149 Author chain E； PDBConstruct 2–150； UniProt 1–149 Author chain F； PDBConstruct 2–150； 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	5e0i
Deposition date deposition_date	2015-09-28
Structure title title	Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution
Keywords keywords	NVR10-001E2, 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.

5e0i__assembly_2__model_1

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

Download this curve (.dat)

5e0i__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5e0i__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.28 Å
Rg (electron density)	34.40 Å
Total Rg	35.20 Å
Atom count	7044
Residues	880
Excluded volume	125880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5e0i__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5e0i__assembly_2__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	17688.2 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	7532

SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVVKLENLYF

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate
Molecular weight formula_weight	493.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	440

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6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (17 domains)

Domain ID domain_id	d5e0ia1
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	d5e0ia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ia3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ib1
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	d5e0ib2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ib3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ic1
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	d5e0ic2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ic3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0id1
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	d5e0id2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ie1
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	d5e0ie2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0ie3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0if1
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	d5e0if2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5e0if3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	5e0iA00
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	5e0iB00
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	5e0iC00
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	5e0iD00
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	5e0iE00
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	5e0iF00
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	152.600 Å
Unit-cell length b length_b	88.170 Å
Unit-cell length c length_c	102.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.47 °
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	1.950 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2520

Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution

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

5e0i__assembly_2__model_1

5e0i__assembly_2__model_1 | I(q)

5e0i__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 (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) 23 domains

SCOP 2.08 (17 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution

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

5e0i__assembly_2__model_1

5e0i__assembly_2__model_1 | I(q)

5e0i__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 (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) 23 domains

SCOP 2.08 (17 domains)

CATH v4.4 (6 domains)

7. Citations (1)