1vbe

POLIOVIRUS (TYPE 3, SABIN STRAIN, MUTANT 242-H2) COMPLEXED WITH R78206

Method: X-RAY DIFFRACTION Dmax: 96.6 Å Quality: GOOD

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

POLIOVIRUS TYPE 3

OrganismNot specified

UniProt P03302

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: complete icosahedral assembly(300) Consistent with protein copy count Chain 1; UniProt 578–877 Chain 2; UniProt 69–339 Chain 3; UniProt 340–574 Chain 4; UniProt 1–68 Mutation:CHAIN 1, F124L, F134L POLIOVIRUS TYPE 3 × 60 J78 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 60 MYR MYRISTIC ACID × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 578–877 Chain 2; UniProt 69–339 Chain 3; UniProt 340–574 Chain 4; UniProt 1–68 Mutation:CHAIN 1, F124L, F134L POLIOVIRUS TYPE 3 × 1 J78 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 1; UniProt 578–877 Chain 2; UniProt 69–339 Chain 3; UniProt 340–574 Chain 4; UniProt 1–68 Mutation:CHAIN 1, F124L, F134L POLIOVIRUS TYPE 3 × 5 J78 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 5 MYR MYRISTIC ACID × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 578–877 Chain 2; UniProt 69–339 Chain 3; UniProt 340–574 Chain 4; UniProt 1–68 Mutation:CHAIN 1, F124L, F134L POLIOVIRUS TYPE 3 × 6 J78 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 6 MYR MYRISTIC ACID × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 578–877 Chain 2; UniProt 69–339 Chain 3; UniProt 340–574 Chain 4; UniProt 1–68 Mutation:CHAIN 1, F124L, F134L POLIOVIRUS TYPE 3 × 1 J78 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å
6 Protein heterocomplex Heteromer Protein × 75 PDB declaration: 75-meric(75) Consistent with protein copy count Chain 1; UniProt 578–877 Chain 2; UniProt 69–339 Chain 3; UniProt 340–574 Chain 4; UniProt 1–68 Mutation:CHAIN 1, F124L, F134L POLIOVIRUS TYPE 3 × 15 J78 (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE × 15 MYR MYRISTIC ACID × 15 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

11 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_POL3L
Isoform
PDB entities 2, 3, 4, 5
Chains and sequence ranges Author chain 1; PDBConstruct 1–300; UniProt 578–877 Author chain 2; PDBConstruct 1–271; UniProt 69–339 Author chain 3; PDBConstruct 1–235; UniProt 340–574 Author chain 4; PDBConstruct 1–68; UniProt 1–68

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1vbe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vbe
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1vbe
Deposition date deposition_date1996-01-02
Structure title titlePOLIOVIRUS (TYPE 3, SABIN STRAIN, MUTANT 242-H2) COMPLEXED WITH R78206
Keywords keywordsVIRUS COAT PROTEIN, HYDROLASE, THIOL PROTEASE, Icosahedral virus, Virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.07
Radius of gyration Rg (electron density) rg_electron29.07
Forward intensity I(0) i0142472000.00
Molecular weight molecular_weight94498.0 kDa
Excluded volume excluded_volume118190 ų
Envelope volume envelope_volume148930 ų
Hydration-shell volume shell_volume41474 ų
Envelope diameter envelope_diameter102.7
Shell Rg shell_rg37.16
Envelope Rg envelope_rg29.76
Shape Rg shape_rg29.05
Total Rg total_rg29.87
Total atoms total_atoms6653
Residues n_residues846
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax96.6
Rg (real space) rg_real29.99
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real1.4250e+08
I(0) uncertainty (real space) i0_real_error1.8900e+06
Rg (reciprocal space) rg_reciprocal30.02
I(0) (reciprocal space) i0_reciprocal142500000.0000
Solution quality estimate total_estimate0.8942
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.5
Skewness Skewness skewness0.289
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29230000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.949

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1vbe.1
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1vbe1_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1vbe3_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (4 domains)

Domain ID domain_id1vbe100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1vbe200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1vbe300
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1vbe400
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4

8. Citations (7)

9. Files and Curves (10)