SAXSdb — 5ddj

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

Foot and mouth disease virus, VP1

Foot-and-mouth disease virus - type O

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 240	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	No other associated polymer	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	No other associated polymer	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6PMW3_9PICO
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–211； UniProt 725–935 Author chain 2； PDBConstruct 1–218； UniProt 287–504 Author chain 3； PDBConstruct 1–220； UniProt 505–724 Author chain 4； PDBConstruct 1–85； UniProt 202–286

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	5ddj
Deposition date deposition_date	2015-08-25
Structure title title	Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid
Keywords keywords	virus, foot and mouth disease virus, picornavirus, aphthovirus, vaccine; 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.

5ddj__assembly_1__model_1

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

Download this curve (.dat)

5ddj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ddj__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	131.60 Å
Atom count	307860
Residues	39600
Excluded volume	5459400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ddj__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ddj__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`5ddj__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`5ddj__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`5ddj__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 (4)

Entity 1 Entity 1 polymer

Description description	Foot and mouth disease virus, VP1
Molecular weight formula_weight	23207.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	5131

TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHTLVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYTAPHRVLATVYNGNSKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRMKRAETYCPRPLLAIHPDQARHKQKIVAPVKQ

Source Source

Source organism organism	Foot-and-mouth disease virus - type O
NCBI taxonomy ID ncbi_taxonomy_id	12118
Host organism host_organism	MESOCRICETUS AURATUS

Entity 2 Entity 2 polymer

Description description	Foot and mouth disease virus, VP2
Molecular weight formula_weight	24417.5 kDa
Mutation mutation	S93Y
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAERFFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGCLLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLVVMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE

Source Source

Source organism organism	Foot-and-mouth disease virus - type O
NCBI taxonomy ID ncbi_taxonomy_id	12118
Host organism host_organism	MESOCRICETUS AURATUS

Entity 3 Entity 3 polymer

Description description	Foot and mouth disease virus, VP3
Molecular weight formula_weight	23905.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLHFEGDVPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKARYMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYAYTASDTAETTNVQGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Source Source

Source organism organism	Foot-and-mouth disease virus - type O
NCBI taxonomy ID ncbi_taxonomy_id	12118
Host organism host_organism	MESOCRICETUS AURATUS

Entity 4 Entity 4 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	8766.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNATSGGSNEGSTDTTSTHTTNTQNNDWFSKLASSAFSGLFGALLA

Source Source

Source organism organism	Foot-and-mouth disease virus - type O
NCBI taxonomy ID ncbi_taxonomy_id	12118
Host organism host_organism	MESOCRICETUS AURATUS

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5ddj100
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5ddj200
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5ddj300
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5ddj400
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	90 — Foot-And-Mouth Disease Virus, subunit 4
Homologous superfamily homologous superfamily	10 — Capsid protein VP4 superfamily, Picornavirus

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Unit-cell length a length_a	344.080 Å
Unit-cell length b length_b	344.080 Å
Unit-cell length c length_c	344.080 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	120

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	49.664 Å
R factor r_factor	—
R_work r_work	0.3610
R_free r_free	—

Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid

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

Foot and mouth disease virus, 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

5ddj__assembly_1__model_1

5ddj__assembly_1__model_1 | I(q)

5ddj__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid

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

Foot and mouth disease virus, 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

5ddj__assembly_1__model_1

5ddj__assembly_1__model_1 | I(q)

5ddj__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)