› 7wku

X-ray diffraction
2.6Å resolution

Structure of PDCoV Mpro in complex with an inhibitor

Released:
DOI: 10.2210/pdb7wku/pdb
PDB entry 7wku coloured by chain, front view.
PDB entry 7wku coloured by chain, side view.
PDB entry 7wku coloured by chain, top view.
Source organisms:
Primary publication:
The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals.
Wang F, Chen C, Wang Z, Han X, Shi P, Zhou K, Liu X, Xiao Y, Cai Y, Huang J, Zhang L, Yang H
OpenAccess logo Viruses 14 (2022)
PMID: 35336895

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102928 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidase C30 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 308 amino acids
Theoretical weight: 34.67 KDa
Source organism: Porcine deltacoronavirus
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A140ESF0 (Residues: 2509-2815; Coverage: 5%)
Sequence domains: Coronavirus endopeptidase C30
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE Chains: H, I, J, K, L, M
Molecule details ›
Chains: H, I, J, K, L, M
Length: 6 amino acids
Theoretical weight: 681 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P61
Unit cell:
a: 122.292Å b: 122.292Å c: 289.754Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.19 0.241
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

In silico identification of natural compounds against SARS-CoV-2 main protease from Chinese herbal medicines.
Kuang et al. (2023)

1 mention without citation

Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses.
Zvornicanin et al. (2023)