› 5n4f

X-ray diffraction
2.4Å resolution

Prolyl oligopeptidase B from Galerina marginata - apo protein

Released:
DOI: 10.2210/pdb5n4f/pdb
PDB entry 5n4f coloured by chain, front view.
PDB entry 5n4f coloured by chain, side view.
PDB entry 5n4f coloured by chain, top view.
Source organism: Galerina marginata
Primary publication:
Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Czekster CM, Ludewig H, McMahon SA, Naismith JH
Nat Commun 8 1045 (2017)
PMID: 29051530

Function and Biology Details

Reaction catalysed: 
Hydrolysis of --Pro-|- and to a lesser extent --Ala-|- in oligopeptides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dual function macrocyclase-peptidase POPB Chain: A
Molecule details ›
Chain: A
Length: 730 amino acids
Theoretical weight: 81.88 KDa
Source organism: Galerina marginata
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H2E7Q8 (Residues: 1-730; Coverage: 100%)
Gene names: GALMADRAFT_78538, POPB
Sequence domains:
Structure domains: alpha/beta hydrolase

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21212
Unit cell:
a: 90.89Å b: 105.62Å c: 86.96Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Biosynthesis of bioactive natural products from Basidiomycota.
Lin et al. (2019)
2 more

4 mentions without citation

Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides.
Ongpipattanakul et al. (2018)
3 more