SAXSdb — 2x5i

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

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	LAURIC ACID × 60	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	LAURIC ACID × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	LAURIC ACID × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	LAURIC ACID × 6	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	LAURIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6W9E5_9ENTO
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 569–860 Author chain B； PDBConstruct 1–260； UniProt 71–330 Author chain C； PDBConstruct 1–238； UniProt 331–568 Author chain D； PDBConstruct 1–70； UniProt 1–70

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	2x5i
Deposition date deposition_date	2010-02-08
Structure title title	Crystal structure echovirus 7
Keywords keywords	VIRUS, CAPSID PROTEIN; 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.

2x5i__assembly_1__model_1

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

Download this curve (.dat)

2x5i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2x5i__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)	131.50 Å
Total Rg	131.50 Å
Atom count	392400
Residues	49680
Excluded volume	6951300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2x5i__assembly_1__model_1`	240-MERIC （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2x5i__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`2x5i__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`2x5i__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`2x5i__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 (5)

Entity 1 Entity 1 polymer

Description description	VP1
Molecular weight formula_weight	33313.2 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	6540

GDTETAIDNAIARVADTVASGPSNSTSIPALTAVETGHTSQVEPSDTMQTRHVKNYHSRSESTVENFLSRSACVYIEEYYTKDQDNVNRYMSWTINARRMVQLRRKFELFTYMRFDMEITFVITSRQLPGTSIAQDMPPLTHQIMYIPPGGPVPNSVTDFAWQTSTNPSIFWTEGNAPPRMSIPFISIGNAYSNFYDGWSHFSQNGVYGYNALNNMGKLYARHVNKDTPYQMSSTIRVYFKPKHIRVWVPRPPRLSPYIKSSNVNFNPTNLTDERSSITYVPDTIRPDVRTN

Entity 2 Entity 2 polymer

Description description	VP2
Molecular weight formula_weight	29072.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PSAEECGYSDRVRSLTLGNSTITTQESANVVVGYGRWPEYLRDDEATAEDQPTQPDVATCRFYTLESVQWEKNSAGWWWKFPEALKDMGLFGQNMLYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGCSQTDKEVAAMNLTKGEAAHKFEPTKTNGEHTVQSIVCNAGMGVGVGNLTIYPHQWINLRTNNCATIVMPYVNSVPMDNMFRHYNFTLMVIPFAPLDYAAQASEYVPVTVTIAPMCAEYNGLRLAYQQ

Entity 3 Entity 3 polymer

Description description	VP3
Molecular weight formula_weight	26227.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GLPVLNTPGSNQFMTSDDFQSPSAMPQFDVTPHMDIPGEVHNLMEIAEVDSVVPVNNIKANLQSMDAYHIEVNTGNYQGEKIFAFQMQPGLESVFKRTLMGEILNYYAHWSGSIKLTFTFCGSAMATGKLLLAYSPPGADVPATRKQAMLGTHMIWDIGLQSSCVLCIPWISQTHYRLVQQDEYTSAGNVTCWYQTGIVVPPGTPNKCVVLCFASACNDFSVRMLRDTPFIGQTALLQ

Entity 4 Entity 4 polymer

Description description	VP4
Molecular weight formula_weight	7599.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGAQVSTQKTGAHETGLNASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMIKTMPALNS

Entity 5 Entity 5 non-polymer

Description description	LAURIC ACID
Molecular weight formula_weight	200.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2x5ia_
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	d2x5ic_
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	2x5iA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2x5iB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2x5iC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2x5iD00
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	297.100 Å
Unit-cell length b length_b	297.700 Å
Unit-cell length c length_c	300.600 Å
Unit-cell angle α angle_alpha	119.00 °
Unit-cell angle β angle_beta	100.10 °
Unit-cell angle γ angle_gamma	108.40 °
Molecules per unit cell Z z_pdb	60

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2882
R_work r_work	0.2882
R_free r_free	—

Crystal structure echovirus 7

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

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

2x5i__assembly_1__model_1

2x5i__assembly_1__model_1 | I(q)

2x5i__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

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

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure echovirus 7

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

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

2x5i__assembly_1__model_1

2x5i__assembly_1__model_1 | I(q)

2x5i__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

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

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)