› 4pdw

X-ray diffraction
3Å resolution

A benzonitrile analogue inhibits rhinovirus replication

Released:
DOI: 10.2210/pdb4pdw/pdb
PDB entry 4pdw coloured by chain, front view.
PDB entry 4pdw coloured by chain, side view.
PDB entry 4pdw coloured by chain, top view.
Source organisms:
Primary publication:
A novel benzonitrile analogue inhibits rhinovirus replication.
Lacroix C, Querol-Audí J, Roche M, Franco D, Froeyen M, Guerra P, Terme T, Vanelle P, Verdaguer N, Neyts J, Leyssen P
J Antimicrob Chemother 69 2723-32 (2014)
PMID: 24948704

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123539 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 289 amino acids
Theoretical weight: 32.56 KDa
Source organism: rhinovirus B14
UniProt:
  • Canonical: P03303 (Residues: 568-856; Coverage: 13%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP2 Chain: B
Molecule details ›
Chain: B
Length: 262 amino acids
Theoretical weight: 28.5 KDa
Source organism: rhinovirus B14
UniProt:
  • Canonical: P03303 (Residues: 70-331; Coverage: 12%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP3 Chain: C
Molecule details ›
Chain: C
Length: 236 amino acids
Theoretical weight: 26.24 KDa
Source organism: rhinovirus B14
UniProt:
  • Canonical: P03303 (Residues: 332-567; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP4/VP2 Chain: D
Molecule details ›
Chain: D
Length: 68 amino acids
Theoretical weight: 7.18 KDa
Source organism: Rhinovirus B
UniProt:
  • Canonical: F5A5A0 (Residues: 2-69; Coverage: 47%)
Sequence domains: Picornavirus coat protein (VP4)
Structure domains: Picornavirus coat protein VP4

Ligands and Environments

2 bound ligands:
Ligand GOL 4 x GOL
Ligand 2XK 1 x 2XK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P213
Unit cell:
a: 439.411Å b: 439.411Å c: 439.411Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.2 0.2

Quick links

Citations

10 citation in other articles

Viral engagement with host receptors blocked by a novel class of tryptophan dendrimers that targets the 5-fold-axis of the enterovirus-A71 capsid.
Sun et al. (2019)
9 more

1 mention without citation

Glutathione facilitates enterovirus assembly by binding at a druggable pocket.
Duyvesteyn et al. (2020)