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4pdw

A benzonitrile analogue inhibits rhinovirus replication

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Genome polyprotein

OrganismNot specified

UniProt P03303

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 240 Capsid protein VP4/VP2 × 60 （F5A5A0） GLYCEROL × 240 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 60 water × 240 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Capsid protein VP4/VP2 × 1 （F5A5A0） GLYCEROL × 4 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 20 Capsid protein VP4/VP2 × 5 （F5A5A0） GLYCEROL × 20 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 5 water × 20 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 24 Capsid protein VP4/VP2 × 6 （F5A5A0） GLYCEROL × 24 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 6 water × 24 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 Capsid protein VP4/VP2 × 1 （F5A5A0） GLYCEROL × 4 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1xr5 2in2 9lgp 9lgp 9lgp 9lgp

6 assemblies

Homodimer

None

Homotetramer
1hri 1hri 1hrv 1hrv 1na1 1na1 1ncq 1ncq 1r08 1r08 1r09 1r09

56 assemblies; showing the first 12

Other homooligomers
1hri 1hri 1hri 1hri 1hrv 1hrv 1hrv 1hrv 1na1 1na1 1na1 1na1

116 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
1d3i 1d3i 1d3i 1d3i 1d3i 1k5m 1k5m 1k5m 1k5m 1k5m 1k5m 1rvf

63 assemblies; showing the first 12

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 240 Genome polyprotein × 60 （P03303） Genome polyprotein × 60 （P03303） Genome polyprotein × 60 （P03303） GLYCEROL × 240 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 60 water × 240 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Genome polyprotein × 1 （P03303） Genome polyprotein × 1 （P03303） Genome polyprotein × 1 （P03303） GLYCEROL × 4 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 20 Genome polyprotein × 5 （P03303） Genome polyprotein × 5 （P03303） Genome polyprotein × 5 （P03303） GLYCEROL × 20 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 5 water × 20 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 24 Genome polyprotein × 6 （P03303） Genome polyprotein × 6 （P03303） Genome polyprotein × 6 （P03303） GLYCEROL × 24 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 6 water × 24 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 Genome polyprotein × 1 （P03303） Genome polyprotein × 1 （P03303） Genome polyprotein × 1 （P03303） GLYCEROL × 4 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4pdw 4pdw 4pdw 4pdw 4pdw

5 assemblies

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.

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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
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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.

4pdw__assembly_1__model_1

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

Download this curve (.dat)

4pdw__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 1011 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4pdw__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）0.00 Å
Rg (electron density)132.20 Å
Total Rg132.20 Å
Atom count377340
Residues48120
Excluded volume6710400 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4pdw__assembly_1__model_1 240-meric （240） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4pdw__assembly_2__model_1 tetrameric （4） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 4pdw__assembly_3__model_1 eicosameric （20） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 4pdw__assembly_4__model_1 24-meric （24） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 4pdw__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 (7)

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6. 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
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7. Citations (1)