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REFINED CRYSTAL STRUCTURE OF HUMAN RHINOVIRUS 16 COMPLEXED WITH VP63843 (PLECONARIL), AN ANTI-PICORNAVIRAL DRUG CURRENTLY IN CLINICAL TRIALS

Source organism: rhinovirus A16
Biochemical function: structural molecule activity
Biological process: not assigned
Cellular component: viral capsid

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EC 3.4.22.29: Picornain 2A

Reaction catalysed:
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
Systematic name:
-
Alternative Name(s):
  • 2A protease
  • 2A proteinase
  • Picornaviral 2A proteinase
  • Picornavirus endopeptidase 2A
  • Poliovirus protease 2A
  • Poliovirus protease 2A-Pro
  • Poliovirus proteinase 2A
  • Protease 2A
  • Proteinase 2A-Pro
  • Rhinovirus protease 2A
  • Y-G proteinase 2A

EC 3.6.1.15: Nucleoside-triphosphate phosphatase

Reaction catalysed:
NTP + H(2)O = NDP + phosphate
Systematic name:
Unspecific diphosphate phosphohydrolase
Alternative Name(s):
  • NTPase
  • Nucleoside 5-triphosphatase
  • Nucleoside triphosphate hydrolase
  • Nucleoside triphosphate phosphohydrolase
  • Nucleoside-5-triphosphate phosphohydrolase
  • Nucleoside-triphosphatase

EC 3.4.22.28: Picornain 3C

Reaction catalysed:
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.
Alternative Name(s):
  • 3C protease
  • 3C proteinase
  • Coxsackievirus 3C proteinase
  • Cysteine proteinase 3C
  • Foot-and-mouth protease 3C
  • Foot-and-mouth-disease virus proteinase 3C
  • Hepatitis A virus 3C proteinase
  • Picornavirus endopeptidase 3C
  • Poliovirus protease 3C
  • Poliovirus proteinase 3C
  • Protease 3C
  • Rhinovirus protease 3C
  • Rhinovirus proteinase 3C
  • Tomato ringspot nepovirus 3C-related protease

EC 2.7.7.48: RNA-directed RNA polymerase

Reaction catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Systematic name:
Nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • 3D polymerase
  • PB1 proteins
  • PB2 proteins
  • Phage f2 replicase
  • Polymerase L
  • Q-beta replicase
  • RDRP
  • RNA nucleotidyltransferase (RNA-directed)
  • RNA replicase
  • RNA synthetase
  • RNA transcriptase
  • RNA-dependent RNA polymerase
  • RNA-dependent RNA replicase
  • RNA-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid replicase
  • Ribonucleic acid-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid-dependent ribonucleic acid polymerase
  • Ribonucleic replicase
  • Ribonucleic synthetase
  • Transcriptase

GO terms

Biochemical function:
Biological process:
  • not assigned
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00073
Domain description: picornavirus capsid protein
Occurring in:
  1. Capsid protein VP1
  2. Capsid protein VP2
  3. Capsid protein VP3
The deposited structure of PDB entry 1c8m contains 1 copy of Pfam domain PF00073 (picornavirus capsid protein) in Capsid protein VP1. Showing 1 copy in chain A [auth 1].
The deposited structure of PDB entry 1c8m contains 1 copy of Pfam domain PF00073 (picornavirus capsid protein) in Capsid protein VP2. Showing 1 copy in chain B [auth 2].
The deposited structure of PDB entry 1c8m contains 1 copy of Pfam domain PF00073 (picornavirus capsid protein) in Capsid protein VP3. Showing 1 copy in chain C [auth 3].

PF02226
Domain description: Picornavirus coat protein (VP4)
Occurring in:
  1. Capsid protein VP4
The deposited structure of PDB entry 1c8m contains 1 copy of Pfam domain PF02226 (Picornavirus coat protein (VP4)) in Capsid protein VP4. Showing 1 copy in chain D [auth 4].

InterPro InterPro annotations
IPR033703
Domain description: Picornavirus/Calicivirus coat protein
Occurring in:
  1. Capsid protein VP1
  2. Capsid protein VP2
  3. Capsid protein VP3
IPR001676
Domain description: Picornavirus capsid
Occurring in:
  1. Capsid protein VP1
  2. Capsid protein VP2
  3. Capsid protein VP3
IPR029053
Domain description: Viral coat protein subunit
Occurring in:
  1. Capsid protein VP1
  2. Capsid protein VP2
  3. Capsid protein VP3
IPR036988
Domain description: Picornavirus coat protein VP4 superfamily
Occurring in:
  1. Capsid protein VP4
IPR003138
Domain description: Picornavirus coat protein VP4
Occurring in:
  1. Capsid protein VP4

Structure domain

CATH CATH domain
2.60.120.20
Class: Mainly Beta
Architecture: Sandwich
Topology: Jelly Rolls
Homology: Jelly Rolls
Occurring in:
  1. Capsid protein VP1
  2. Capsid protein VP2
  3. Capsid protein VP3
The deposited structure of PDB entry 1c8m contains 1 copy of CATH domain 2.60.120.20 (Jelly Rolls) in Capsid protein VP1. Showing 1 copy in chain A [auth 1].
The deposited structure of PDB entry 1c8m contains 1 copy of CATH domain 2.60.120.20 (Jelly Rolls) in Capsid protein VP2. Showing 1 copy in chain B [auth 2].
The deposited structure of PDB entry 1c8m contains 1 copy of CATH domain 2.60.120.20 (Jelly Rolls) in Capsid protein VP3. Showing 1 copy in chain C [auth 3].
SCOP SCOP annotation
88634
Class: All beta proteins
Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily: Positive stranded ssRNA viruses
Occurring in:
  1. Capsid protein VP1
  2. Capsid protein VP2
  3. Capsid protein VP3
  4. Capsid protein VP4
The deposited structure of PDB entry 1c8m contains 1 copy of SCOP domain 88634 (Picornaviridae-like VP (VP1, VP2, VP3 and VP4)) in Capsid protein VP1. Showing 1 copy in chain A [auth 1].
The deposited structure of PDB entry 1c8m contains 1 copy of SCOP domain 88634 (Picornaviridae-like VP (VP1, VP2, VP3 and VP4)) in Capsid protein VP2. Showing 1 copy in chain B [auth 2].
The deposited structure of PDB entry 1c8m contains 1 copy of SCOP domain 88634 (Picornaviridae-like VP (VP1, VP2, VP3 and VP4)) in Capsid protein VP3. Showing 1 copy in chain C [auth 3].

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