› 4qme

X-ray diffraction
1.6Å resolution

Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe

Released:
DOI: 10.2210/pdb4qme/pdb
PDB entry 4qme coloured by chain, front view.
PDB entry 4qme coloured by chain, side view.
PDB entry 4qme coloured by chain, top view.
Source organism: Neisseria meningitidis MC58
Primary publication:
Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases.
Vassiliou S, Węglarz-Tomczak E, Berlicki Ł, Pawełczak M, Nocek B, Mulligan R, Joachimiak A, Mucha A
OpenAccess logo J Med Chem 57 8140-51 (2014)
PMID: 25192493

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191698 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminopeptidase N Chain: A
Molecule details ›
Chain: A
Length: 866 amino acids
Theoretical weight: 98.51 KDa
Source organism: Neisseria meningitidis MC58
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JYV4 (Residues: 2-867; Coverage: 100%)
Gene names: NMB1416, pepN
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand 37B 1 x 37B
Ligand ZN 1 x ZN
Ligand GOL 2 x GOL
Ligand IMD 2 x IMD
Ligand SO4 7 x SO4
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: R3
Unit cell:
a: 224Å b: 224Å c: 57.872Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.15 0.144 0.172
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Asymmetric Synthesis of Tetrasubstituted α-Aminophosphonic Acid Derivatives.
Maestro et al. (2021)
1 more

2 mentions without citation

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.
Louder et al. (2016)
1 more