› 2r04

X-ray diffraction
3Å resolution

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES

Released:
DOI: 10.2210/pdb2r04/pdb
PDB entry 2r04 coloured by chain, front view.
PDB entry 2r04 coloured by chain, side view.
PDB entry 2r04 coloured by chain, top view.
Source organism: rhinovirus B14
Primary publication:
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.
Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG
Proteins 6 1-19 (1989)
PMID: 2558377

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 domain:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136741 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Capsid protein VP1 Chain: 1
Molecule details ›
Chain: 1
Length: 289 amino acids
Theoretical weight: 32.56 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 568-856; Coverage: 13%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP2 Chain: 2
Molecule details ›
Chain: 2
Length: 262 amino acids
Theoretical weight: 28.5 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 70-331; Coverage: 12%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP3 Chain: 3
Molecule details ›
Chain: 3
Length: 236 amino acids
Theoretical weight: 26.24 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 332-567; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP4 Chain: 4
Molecule details ›
Chain: 4
Length: 68 amino acids
Theoretical weight: 7.18 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 2-69; Coverage: 3%)
Sequence domains: Picornavirus coat protein (VP4)
Structure domains: Picornavirus coat protein VP4

Ligands and Environments

1 bound ligand:
Ligand W71 1 x W71
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P213
Unit cell:
a: 445.1Å b: 445.1Å c: 445.1Å
α: 90° β: 90° γ: 90°
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Selective inhibitors of picornavirus replication.
De Palma et al. (2008)
3 more

5 mentions without citation

Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock.
Bikadi et al. (2009)
4 more