SAXSdb — 7k5m

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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 2	N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide × 2 ISOPROPYL ALCOHOL × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide × 2 ISOPROPYL ALCOHOL × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide × 2 ISOPROPYL ALCOHOL × 2 water × 1	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	7k5m
Deposition date deposition_date	2020-09-17
Structure title title	CRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH N-(3-chloro-4-fluorophenyl)-3-phenyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide AT 2.65A RESOLUTION
Keywords keywords	HVB capsid, 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.

7k5m__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7k5m__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7k5m__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	20.87 Å
Rg (electron density)	20.39 Å
Total Rg	21.06 Å
Atom count	2013
Residues	253
Excluded volume	36000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7k5m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7k5m__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7k5m__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 (4)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	17816.3 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	6216

SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVVKLENLYFQ

Source Source

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)

Entity 2 Entity 2 non-polymer

Description description	N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide
Molecular weight formula_weight	370.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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Unit-cell length a length_a	151.580 Å
Unit-cell length b length_b	87.960 Å
Unit-cell length c length_c	106.710 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.53 °
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	2.650 Å
Low-resolution limit resolution_low	48.035 Å
R factor r_factor	0.2442
R_work r_work	0.2424
R_free r_free	0.2757

CRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH N-(3-chloro-4-fluorophenyl)-3-phenyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide AT 2.65A 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

7k5m__assembly_3__model_1

7k5m__assembly_3__model_1 | I(q)

7k5m__assembly_3__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 (4)

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 water

7. Citations (1)

CRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH N-(3-chloro-4-fluorophenyl)-3-phenyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide AT 2.65A 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

7k5m__assembly_3__model_1

7k5m__assembly_3__model_1 | I(q)

7k5m__assembly_3__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 (4)

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 water

7. Citations (1)