SAXSdb — 8khu

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

Capsid protein

Hepatitis B virus adw/991

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 7	ISOPROPYL ALCOHOL × 7 ;(6~{S},7~{R})-6,7-dimethyl-3-(2-oxidanylidenepyrrolidin-1-yl)-~{N}-[3,4,5-tris(fluoranyl)phenyl]-6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazine-5-carboxamide ; × 6 GLYCEROL × 1 water × 7	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 Author chain G； 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	8khu
Deposition date deposition_date	2023-08-22
Structure title title	Hepatitis B virus core protein Y132A mutant in complex with THPP derivatives 48
Keywords keywords	HBV capsid assembly mudulator, ANTIVIRAL PROTEIN, 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.

8khu__assembly_1__model_1

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

Download this curve (.dat)

8khu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8khu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.38 Å
Rg (electron density)	33.52 Å
Total Rg	34.11 Å
Atom count	7213
Residues	882
Excluded volume	129130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8khu__assembly_1__model_1`	heptameric （7）	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 (5)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	17486.9 kDa
Mutation mutation	Y132A
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	7565

MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVVENLYFQ

Source Source

Source organism organism	Hepatitis B virus adw/991
NCBI taxonomy ID ncbi_taxonomy_id	10410
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	;(6~{S},7~{R})-6,7-dimethyl-3-(2-oxidanylidenepyrrolidin-1-yl)-~{N}-[3,4,5-tris(fluoranyl)phenyl]-6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazine-5-carboxamide ;
Molecular weight formula_weight	407.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	301

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Unit-cell length a length_a	66.207 Å
Unit-cell length b length_b	65.983 Å
Unit-cell length c length_c	86.412 Å
Unit-cell angle α angle_alpha	68.62 °
Unit-cell angle β angle_beta	68.42 °
Unit-cell angle γ angle_gamma	83.33 °
Molecules per unit cell Z z_pdb	7

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	43.040 Å
R factor r_factor	0.1800
R_work r_work	0.1792
R_free r_free	0.2131

Hepatitis B virus core protein Y132A mutant in complex with THPP derivatives 48

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

8khu__assembly_1__model_1

8khu__assembly_1__model_1 | I(q)

8khu__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Hepatitis B virus core protein Y132A mutant in complex with THPP derivatives 48

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

8khu__assembly_1__model_1

8khu__assembly_1__model_1 | I(q)

8khu__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)