SAXSdb — 5d7y

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

Capsid protein

Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 240	;methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate ; × 120	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	;methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate ; × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	;methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate ; × 10	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	;methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate ; × 12	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	;methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate ; × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 240	;methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate ; × 120	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

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	5d7y
Deposition date deposition_date	2015-08-14
Structure title title	Crystal structure of Hepatitis B virus T=4 capsid in complex with the allosteric modulator HAP18
Keywords keywords	;capsid, core protein, hepadnavirus, icosahedral, assembly effector, assembly accelerator, allosteric modulator, HAP, VIRUS-INHIBITOR complex ;; VIRUS/INHIBITOR
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.

5d7y__assembly_1__model_1

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

Download this curve (.dat)

5d7y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5d7y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	147.60 Å
Total Rg	147.70 Å
Atom count	276600
Residues	34200
Excluded volume	4953600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5d7y__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5d7y__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`5d7y__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`5d7y__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`5d7y__assembly_5__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`5d7y__assembly_6__model_1`	240-meric （240）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5d7yA00
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	5d7yB00
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	5d7yC00
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	5d7yD00
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	529.375 Å
Unit-cell length b length_b	367.411 Å
Unit-cell length c length_c	542.002 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	960

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

Resolution resolution	3.894 Å
Low-resolution limit resolution_low	35.682 Å
R factor r_factor	0.2626
R_work r_work	0.2626
R_free r_free	0.2732

Description description	Capsid protein
Molecular weight formula_weight	16823.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4610

Crystal structure of Hepatitis B virus T=4 capsid in complex with the allosteric modulator HAP18

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

5d7y__assembly_1__model_1

5d7y__assembly_1__model_1 | I(q)

5d7y__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 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)
Common name common_name	HBV-D
NCBI taxonomy ID ncbi_taxonomy_id	10419
Host organism host_organism	Escherichia coli BL21(DE3)

Crystal structure of Hepatitis B virus T=4 capsid in complex with the allosteric modulator HAP18

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

5d7y__assembly_1__model_1

5d7y__assembly_1__model_1 | I(q)

5d7y__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 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)