› 4re6

X-ray diffraction
2.55Å resolution

Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor

Released:
DOI: 10.2210/pdb4re6/pdb
PDB 4re6 coloured by chain and viewed from the front.
PDB 4re6 coloured by chain and viewed from the side.
PDB 4re6 coloured by chain and viewed from the top.
Source organism: Aeropyrum pernix K1
Primary publication:
Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality.
Menyh��rd DK, Orgov��n Z, Szeltner Z, Szamosi I, Harmat V
Acta Crystallogr. D Biol. Crystallogr. 71 461-72 (2015)
PMID: 25760596

Function and Biology Details

Reaction catalysed: 
Cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Acylamino-acid-releasing enzyme Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 582 amino acids
Theoretical weight: 63.11 KDa
Source organism: Aeropyrum pernix K1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YBQ2 (Residues: 1-582; Coverage: 100%)
Gene name: APE_1547.1
Sequence domains: Prolyl oligopeptidase family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand Y3A 2 x Y3A
Ligand CL 6 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P1
Unit cell:
a: 71.58Å b: 97.3Å c: 99.16Å
α: 105.15° β: 103.96° γ: 100.26°
R-values:
R R work R free
0.214 0.212 0.26
Expression system: Escherichia coli

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Citations

6 citation in other articles

Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolase.
Ishikawa et al. (2017)
5 more