SAXSdb — 4wyj

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

Fiber protein

Human adenovirus B serotype 3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 10 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_ADE03
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–194； UniProt 127–319 Author chain B； PDBConstruct 2–194； UniProt 127–319 Author chain C； PDBConstruct 2–194； UniProt 127–319

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	4wyj
Deposition date deposition_date	2014-11-17
Structure title title	Adenovirus 3 head domain mutant V239D
Keywords keywords	adenovirus head domain, 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.

4wyj__assembly_1__model_1

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

Download this curve (.dat)

4wyj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wyj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.25 Å
Rg (electron density)	23.54 Å
Total Rg	24.63 Å
Atom count	4484
Residues	566
Excluded volume	79751 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wyj__assembly_1__model_1`	trimeric （3）	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	Fiber protein
Molecular weight formula_weight	21601.4 kDa
Mutation mutation	V239D
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4737

MALKNNTLWTGPKPEANCIIEYGKQNPDSKLTLILVKNGGIVNGYVTLMGASDYVNTLFKNKNVSINVELYFDATGHILPDSSSLKTDLELKYKQTADFSARGFMPSTTAYPFDLPNAGTHNENYIFGQCYYKASDGALFPLEVTVMLNKRLPDSRTSYVMTFLWSLNAGLAPETTQATLITSPFTFSYIREDD

Source Source

Source organism organism	Human adenovirus B serotype 3
Common name common_name	HAdV-3
NCBI taxonomy ID ncbi_taxonomy_id	45659
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	245

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4wyja_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d4wyjb_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d4wyjc_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

CATH v4.4 (3 domains)

Domain ID domain_id	4wyjA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	4wyjB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	4wyjC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

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Unit-cell length a length_a	137.566 Å
Unit-cell length b length_b	137.566 Å
Unit-cell length c length_c	108.939 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	44.410 Å
R factor r_factor	0.1772
R_work r_work	0.1757
R_free r_free	0.2049

Adenovirus 3 head domain mutant V239D

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

Fiber 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

4wyj__assembly_1__model_1

4wyj__assembly_1__model_1 | I(q)

4wyj__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 (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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Adenovirus 3 head domain mutant V239D

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

Fiber 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

4wyj__assembly_1__model_1

4wyj__assembly_1__model_1 | I(q)

4wyj__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 (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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)