SAXSdb — 1oop

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

Coat protein VP1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 240	SPHINGOSINE × 60 MYRISTIC ACID × 60	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SPHINGOSINE × 1 MYRISTIC ACID × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	SPHINGOSINE × 5 MYRISTIC ACID × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	SPHINGOSINE × 6 MYRISTIC ACID × 6	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	SPHINGOSINE × 1 MYRISTIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_SVDVU
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 569–851 Author chain B； PDBConstruct 1–261； UniProt 70–330 Author chain C； PDBConstruct 1–238； UniProt 331–568 Author chain D； PDBConstruct 1–69； UniProt 1–69

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	1oop
Deposition date deposition_date	2003-03-04
Structure title title	The Crystal Structure of Swine Vesicular Disease Virus
Keywords keywords	;PICORNAVIRUS STRUCTURE, VIRUS/VIRAL PROTEIN, VIRUS-RECEPTOR INTERACTIONS, HOST ADAPTATION, CAR, DAF, COXSACKIEVIRUS, Icosahedral virus, Virus ;; 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.

1oop__assembly_1__model_1

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

Download this curve (.dat)

1oop__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1oop__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)	132.30 Å
Total Rg	132.30 Å
Atom count	383940
Residues	49140
Excluded volume	6810400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1oop__assembly_1__model_1`	complete icosahedral assembly （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1oop__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1oop__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1oop__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1oop__assembly_5__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Coat protein VP1
Molecular weight formula_weight	31538.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6399

GPPGEVMGRAIARVADTIGSGPVNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTVENFLCRSACVFYTTYENHDSDGDNFAYWVINTRQVAQLRRKLEMFTYARFDLELTFVITSTQEQPTVRGQDAPVLTHQIMYVPPGGPVPTKVNSYSWQTSTNPSVFWTEGSAPPRMSVPFIGIGNAYSMFYDGWARFDKQGTYGISTLNNMGTLYMRHVNDGGPGPIVSTVRIYFKPKHVKTWVPRPPRLCQYQKAGNVNFEPTGVTEGRTDITTMKTT

Entity 2 Entity 2 polymer

Description description	Coat protein VP2
Molecular weight formula_weight	28652.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPSAEECGYSDRVRSITLGNSTITTQECANVVVGYGVWPTYLKDEEATAEDQPTQPDVATCRFYTLESVMWQQSSPGWWWKFPDALSNMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGCATLANKPDPKSLSKGEIANMFESQNSTGETAVQANVINAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNFTLMVIPFAPLSYSTGATTYVPITVTVAPMCAEYNGLRLAGKQ

Entity 3 Entity 3 polymer

Description description	Coat protein VP3
Molecular weight formula_weight	26084.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GLPTLSTPGSNQFLTSDDFQSPSAMPQFDVTPEMDIPGQVNNLMEIAEVDSVVPVNNTEGKVMSIEAYQIPVQSNPTNGSQVFGFPLTPGANSVLNRTLLGEILNYYAHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTTRKEAMLGTHVIWDVGLQSSCVLCIPWISQTHYRYVVMDEYTAGGYITCWYQTNIVVPADAQSDCKILCFVSACNDFSVRMLKDTPFIKQDNFFQ

Entity 4 Entity 4 polymer

Description description	Coat protein VP4
Molecular weight formula_weight	7457.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGAQVSTQKTGAHETSLSAAGNSVIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMVKSMPALN

Entity 5 Entity 5 non-polymer

Description description	SPHINGOSINE
Molecular weight formula_weight	299.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1oop.1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1oopa_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1oopc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (4 domains)

Domain ID domain_id	1oopA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1oopB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1oopC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1oopD00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	10 — Picornavirus coat protein VP4

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Unit-cell length a length_a	354.100 Å
Unit-cell length b length_b	371.700 Å
Unit-cell length c length_c	318.600 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2450
R_work r_work	—
R_free r_free	—

The Crystal Structure of Swine Vesicular Disease Virus

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

Coat protein VP1

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

1oop__assembly_1__model_1

1oop__assembly_1__model_1 | I(q)

1oop__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

The Crystal Structure of Swine Vesicular Disease Virus

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

Coat protein VP1

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

1oop__assembly_1__model_1

1oop__assembly_1__model_1 | I(q)

1oop__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)