› 2q6f

X-ray diffraction
2Å resolution

Crystal structure of infectious bronchitis virus (IBV) main protease in complex with a Michael acceptor inhibitor N3

Released:
DOI: 10.2210/pdb2q6f/pdb
PDB entry 2q6f coloured by chain, front view.
PDB entry 2q6f coloured by chain, side view.
PDB entry 2q6f coloured by chain, top view.
Source organisms:
Primary publication:
Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design.
Xue X, Yu H, Yang H, Xue F, Wu Z, Shen W, Li J, Zhou Z, Ding Y, Zhao Q, Zhang XC, Liao M, Bartlam M, Rao Z
J Virol 82 2515-27 (2008)
PMID: 18094151

Function and Biology Details

Reaction catalysed: 
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).
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143089 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
3C-like proteinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 309 amino acids
Theoretical weight: 33.64 KDa
Source organism: Infectious bronchitis virus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0C6V5 (Residues: 2782-3088; Coverage: 8%)
Gene name: 1a
Sequence domains: Coronavirus endopeptidase C30
Structure domains:
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: C, D
Molecule details ›
Chains: C, D
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: RIGAKU MICROMAX-007
Spacegroup: P1
Unit cell:
a: 53.175Å b: 54.502Å c: 66.719Å
α: 111.06° β: 104.31° γ: 91.33°
R-values:
R R work R free
0.218 0.216 0.242
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

62 review citations

The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds.
Báez-Santos et al. (2015)
61 more

15 mentions without citation

Atlas of coronavirus replicase structure.
Neuman et al. (2014)
14 more