› 5mfr

X-ray diffraction
1.4Å resolution

The crystal structure of E. coli Aminopeptidase N in complex with 7-amino-5,7,8,9-tetrahydrobenzocyclohepten-6-one

Released:
DOI: 10.2210/pdb5mfr/pdb
PDB entry 5mfr coloured by chain, front view.
PDB entry 5mfr coloured by chain, side view.
PDB entry 5mfr coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis.
Peng G, McEwen AG, Olieric V, Schmitt C, Albrecht S, Cavarelli J, Tarnus C
Proteins 85 1413-1421 (2017)
PMID: 28383176

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal amino acid, Xaa-|-Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-528823 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminopeptidase N Chain: A
Molecule details ›
Chain: A
Length: 891 amino acids
Theoretical weight: 101.44 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04825 (Residues: 1-870; Coverage: 100%)
Gene names: JW0915, b0932, pepN
Sequence domains:
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand ZN 1 x ZN
Ligand 7MK 1 x 7MK
Ligand GOL 10 x GOL
Ligand NA 8 x NA
Ligand MLI 4 x MLI
Ligand DMS 2 x DMS
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P3121
Unit cell:
a: 120.755Å b: 120.755Å c: 170.695Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.104 0.104 0.127
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

IRAP Inhibitors: M1-Aminopeptidase Family Inspiration.
Barlow et al. (2020)
2 other articles

2 mentions without citation

Marine Invertebrates: A Promissory Still Unexplored Source of Inhibitors of Biomedically Relevant Metallo Aminopeptidases Belonging to the M1 and M17 Families.
Pascual Alonso et al. (2023)
1 more