› 5t6d

X-ray diffraction
2.1Å resolution

2.10 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 7l (hexagonal form)

Released:
DOI: 10.2210/pdb5t6d/pdb
PDB entry 5t6d coloured by chain, front view.
PDB entry 5t6d coloured by chain, side view.
PDB entry 5t6d coloured by chain, top view.
Source organism: Norovirus Hu/1968/US
Primary publication:
Structure-based exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors.
Galasiti Kankanamalage AC, Kim Y, Rathnayake AD, Damalanka VC, Weerawarna PM, Doyle ST, Alsoudi AF, Dissanayake DMP, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC
Eur J Med Chem 126 502-516 (2017)
PMID: 27914364

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182856 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 188 amino acids
Theoretical weight: 20.13 KDa
Source organism: Norovirus Hu/1968/US
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q83883 (Residues: 1101-1281; Coverage: 10%)
Gene name: ORF1
Structure domains: Trypsin-like serine proteases

Ligands and Environments

1 bound ligand:
Ligand N38 2 x N38
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P6122
Unit cell:
a: 59.53Å b: 59.53Å c: 356.804Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.193 0.243
Expression system: Escherichia coli BL21

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Citations

1 review citation

Antiviral Drug Discovery: Norovirus Proteases and Development of Inhibitors.
Chang et al. (2019)
9 other articles

4 mentions without citation

Structure-based exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors.
Galasiti Kankanamalage et al. (2017)
3 more