SAXSdb — 1vbd

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

POLIOVIRUS TYPE 1 MAHONEY

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 300	POLIOVIRUS TYPE 1 MAHONEY × 60 POLIOVIRUS TYPE 1 MAHONEY × 60 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 60 MYRISTIC ACID × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	POLIOVIRUS TYPE 1 MAHONEY × 1 POLIOVIRUS TYPE 1 MAHONEY × 1 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 1 MYRISTIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 25	POLIOVIRUS TYPE 1 MAHONEY × 5 POLIOVIRUS TYPE 1 MAHONEY × 5 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 5 MYRISTIC ACID × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 30	POLIOVIRUS TYPE 1 MAHONEY × 6 POLIOVIRUS TYPE 1 MAHONEY × 6 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 6 MYRISTIC ACID × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 5	POLIOVIRUS TYPE 1 MAHONEY × 1 POLIOVIRUS TYPE 1 MAHONEY × 1 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 1 MYRISTIC ACID × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 150	POLIOVIRUS TYPE 1 MAHONEY × 30 POLIOVIRUS TYPE 1 MAHONEY × 30 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 30 MYRISTIC ACID × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLH_POL1M
Isoform	—
PDB entities	2, 3, 4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–302； UniProt 579–880 Author chain 2； PDBConstruct 1–272； UniProt 69–340 Author chain 3； PDBConstruct 1–238； UniProt 341–578

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	1vbd
Deposition date deposition_date	1996-01-02
Structure title title	POLIOVIRUS (TYPE 1, MAHONEY STRAIN) COMPLEXED WITH R78206
Keywords keywords	VIRUS COAT PROTEIN, HYDROLASE, THIOL PROTEASE, 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.

1vbd__assembly_1__model_1

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

Download this curve (.dat)

1vbd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vbd__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)	132.70 Å
Total Rg	132.80 Å
Atom count	400500
Residues	51060
Excluded volume	7114300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vbd__assembly_1__model_1`	300-MERIC （300）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vbd__assembly_2__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1vbd__assembly_3__model_1`	25-meric （25）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1vbd__assembly_4__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1vbd__assembly_5__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1vbd__assembly_6__model_1`	150-meric （150）	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 (7)

Entity 1 Entity 1 polymer

Description description	POLIOVIRUS TYPE 1 MAHONEY
Molecular weight formula_weight	437.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0
Atom count atom_count	6675

GSSST

Entity 2 Entity 2 polymer

Description description	POLIOVIRUS TYPE 1 MAHONEY
Molecular weight formula_weight	33488.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

GLGQMLESMIDNTVRETVGAATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDTVQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY

Entity 3 Entity 3 polymer

Description description	POLIOVIRUS TYPE 1 MAHONEY
Molecular weight formula_weight	30075.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

SPNIEACGYSDRVLQLTLGNSTITTQEAANSVVAYGRWPEYLRDSEANPVDQPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITLTIAPMCCEFNGLRNITLPRLQ

Entity 4 Entity 4 polymer

Description description	POLIOVIRUS TYPE 1 MAHONEY
Molecular weight formula_weight	26547.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKALAQ

Entity 5 Entity 5 polymer

Description description	POLIOVIRUS TYPE 1 MAHONEY
Molecular weight formula_weight	7393.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

GAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLN

Entity 6 Entity 6 non-polymer

Description description	(METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE
Molecular weight formula_weight	383.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 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	d1vbd.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	d1vbd1_
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	d1vbd3_
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	1vbd100
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1vbd200
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1vbd300
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1vbd400
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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7. Citations (7)

Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design.

Curr.Biol. (1994)

PMID: 7820548 · DOI: 10.1016/S0960-9822(00)00176-7 PRIMARY

;Binding of the Antiviral Drug Win51711 to the Sabin Strain of Type 3 Poliovirus: Structural Comparison with Drug Binding in Rhinovirus 14 ;

Acta Crystallogr.,Sect.D (1995)

Role of Conformational Transitions in Poliovirus Assembly and Cell Entry

New Aspects of Positive-Strand RNA Viruses (1990)

Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus

Embo J. (1989)

Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance

Nature (1987)

Three-Dimensional Structure of Poliovirus at 2.9 A Resolution

Science (1985)

The Nucleotide Sequence of Poliovirus Type 3 Leon 12 A1B: Comparison with Poliovirus Type 1

Nucleic Acids Res. (1983)

Unit-cell length a length_a	322.940 Å
Unit-cell length b length_b	358.040 Å
Unit-cell length c length_c	380.150 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	0.2870
R_free r_free	—

POLIOVIRUS (TYPE 1, MAHONEY STRAIN) COMPLEXED WITH R78206

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

POLIOVIRUS TYPE 1 MAHONEY

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

1vbd__assembly_1__model_1

1vbd__assembly_1__model_1 | I(q)

1vbd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (7)

POLIOVIRUS (TYPE 1, MAHONEY STRAIN) COMPLEXED WITH R78206

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

POLIOVIRUS TYPE 1 MAHONEY

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

1vbd__assembly_1__model_1

1vbd__assembly_1__model_1 | I(q)

1vbd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (7)