4pdw

A benzonitrile analogue inhibits rhinovirus replication

Method: X-RAY DIFFRACTION Dmax: 95.1 Å Quality: GOOD

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

Genome polyprotein

OrganismNot specified

UniProt P03303

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 × 240 PDB declaration: 240-meric(240) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–331 Chain C; UniProt 332–567 Fragment:resdiues 568-856 Fragment:resdiues 70-331 Fragment:resdiues 332-657 Capsid protein VP4/VP2 × 60 (F5A5A0) GOL GLYCEROL × 240 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 60 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–331 Chain C; UniProt 332–567 Fragment:resdiues 568-856 Fragment:resdiues 70-331 Fragment:resdiues 332-657 Capsid protein VP4/VP2 × 1 (F5A5A0) GOL GLYCEROL × 4 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
3 Protein heterocomplex Heteromer Protein × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–331 Chain C; UniProt 332–567 Fragment:resdiues 568-856 Fragment:resdiues 70-331 Fragment:resdiues 332-657 Capsid protein VP4/VP2 × 5 (F5A5A0) GOL GLYCEROL × 20 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
4 Protein heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–331 Chain C; UniProt 332–567 Fragment:resdiues 568-856 Fragment:resdiues 70-331 Fragment:resdiues 332-657 Capsid protein VP4/VP2 × 6 (F5A5A0) GOL GLYCEROL × 24 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
5 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–331 Chain C; UniProt 332–567 Fragment:resdiues 568-856 Fragment:resdiues 70-331 Fragment:resdiues 332-657 Capsid protein VP4/VP2 × 1 (F5A5A0) GOL GLYCEROL × 4 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200

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.

58 other PDB entries and 236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV14
Isoform
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A; PDBConstruct 1–289; UniProt 568–856 Author chain B; PDBConstruct 1–262; UniProt 70–331 Author chain C; PDBConstruct 1–236; UniProt 332–567

Capsid protein VP4/VP2

OrganismNot specified

UniProt F5A5A0

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 × 240 PDB declaration: 240-meric(240) Consistent with protein copy count Chain D; UniProt 2–69 Fragment:residue 2-69 Genome polyprotein × 60 (P03303) Genome polyprotein × 60 (P03303) Genome polyprotein × 60 (P03303) GOL GLYCEROL × 240 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 60 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 2–69 Fragment:residue 2-69 Genome polyprotein × 1 (P03303) Genome polyprotein × 1 (P03303) Genome polyprotein × 1 (P03303) GOL GLYCEROL × 4 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
3 Protein heterocomplex Heteromer Protein × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain D; UniProt 2–69 Fragment:residue 2-69 Genome polyprotein × 5 (P03303) Genome polyprotein × 5 (P03303) Genome polyprotein × 5 (P03303) GOL GLYCEROL × 20 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
4 Protein heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain D; UniProt 2–69 Fragment:residue 2-69 Genome polyprotein × 6 (P03303) Genome polyprotein × 6 (P03303) Genome polyprotein × 6 (P03303) GOL GLYCEROL × 24 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200
5 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 2–69 Fragment:residue 2-69 Genome polyprotein × 1 (P03303) Genome polyprotein × 1 (P03303) Genome polyprotein × 1 (P03303) GOL GLYCEROL × 4 2XK 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;293.15 K;PEG 8000, calcium chloride Resolution 3.00 Å R-free 0.200

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name F5A5A0_9ENTO
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–68; UniProt 2–69

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4pdw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4pdw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4pdw
Deposition date deposition_date2014-04-22
Structure title titleA benzonitrile analogue inhibits rhinovirus replication
Keywords keywordsbenzonitrile inhibitor, virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.51
Radius of gyration Rg (electron density) rg_electron28.45
Forward intensity I(0) i0126326000.00
Molecular weight molecular_weight89288.0 kDa
Excluded volume excluded_volume111840 ų
Envelope volume envelope_volume136390 ų
Hydration-shell volume shell_volume39183 ų
Envelope diameter envelope_diameter101.6
Shell Rg shell_rg36.33
Envelope Rg envelope_rg29.19
Shape Rg shape_rg28.46
Total Rg total_rg29.15
Total atoms total_atoms6289
Residues n_residues802
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 dmax95.1
Rg (real space) rg_real29.48
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real1.2630e+08
I(0) uncertainty (real space) i0_real_error1.8170e+06
Rg (reciprocal space) rg_reciprocal29.49
I(0) (reciprocal space) i0_reciprocal126300000.0000
Solution quality estimate total_estimate0.8904
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.2
Skewness Skewness skewness0.357
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24140000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.913

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4pdwa_
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_idd4pdwc_
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_id4pdwA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id4pdwB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id4pdwC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id4pdwD00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4

8. Citations (1)

9. Files and Curves (10)