SAXSdb — 5egc

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

Capsid protein

Adeno-associated virus - 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	N-acetyl-alpha-neuraminic acid × 60 MAGNESIUM ION × 60 water × 60	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-acetyl-alpha-neuraminic acid × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	N-acetyl-alpha-neuraminic acid × 5 MAGNESIUM ION × 5 water × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	N-acetyl-alpha-neuraminic acid × 6 MAGNESIUM ION × 6 water × 6	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	N-acetyl-alpha-neuraminic acid × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 30	N-acetyl-alpha-neuraminic acid × 30 MAGNESIUM ION × 30 water × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WBP8_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–520； UniProt 217–736

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	5egc
Deposition date deposition_date	2015-10-27
Structure title title	Structure of the Adeno-Associated Virus Serotype 1 sialic acid complex
Keywords keywords	Adeno-Associated Virus 1, single-stranded DNA virus, parvovirus, icosahedral virus, virus, glycan receptor, sialic acid; VIRUS
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.

5egc__assembly_1__model_1

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

Download this curve (.dat)

5egc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5egc__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)	109.10 Å
Total Rg	109.40 Å
Atom count	248520
Residues	31200
Excluded volume	4354600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5egc__assembly_1__model_1`	60-meric （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5egc__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`5egc__assembly_3__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`5egc__assembly_4__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`5egc__assembly_5__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`5egc__assembly_6__model_1`	30-meric （30）	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 (4)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	58356.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4161

GADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL

Source Source

Source organism organism	Adeno-associated virus - 1
NCBI taxonomy ID ncbi_taxonomy_id	85106
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	N-acetyl-alpha-neuraminic acid
Molecular weight formula_weight	309.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5egca_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

CATH v4.4 (1 domains)

Domain ID domain_id	5egcA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

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Unit-cell length a length_a	455.627 Å
Unit-cell length b length_b	261.749 Å
Unit-cell length c length_c	450.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	240

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

Resolution resolution	3.011 Å
Low-resolution limit resolution_low	49.923 Å
R factor r_factor	0.2688
R_work r_work	0.2688
R_free r_free	0.2764

Structure of the Adeno-Associated Virus Serotype 1 sialic acid complex

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

5egc__assembly_1__model_1

5egc__assembly_1__model_1 | I(q)

5egc__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 (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

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of the Adeno-Associated Virus Serotype 1 sialic acid complex

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

5egc__assembly_1__model_1

5egc__assembly_1__model_1 | I(q)

5egc__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 (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

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)