› 4dyo

X-ray diffraction
2.2Å resolution

Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid Hydroxamate

Released:
DOI: 10.2210/pdb4dyo/pdb
PDB entry 4dyo coloured by chain, front view.
PDB entry 4dyo coloured by chain, side view.
PDB entry 4dyo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family.
Chaikuad A, Pilka ES, De Riso A, von Delft F, Kavanagh KL, Vénien-Bryan C, Oppermann U, Yue WW
BMC Struct Biol 12 14 (2012)
PMID: 22720794

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal aspartate or glutamate from a peptide, with a preference for aspartate.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dodecamer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193916 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aspartyl aminopeptidase Chain: A
Molecule details ›
Chain: A
Length: 485 amino acids
Theoretical weight: 53.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9ULA0 (Residues: 11-478; Coverage: 97%)
Gene names: ASPEP, DAP, DNPEP
Sequence domains: Aminopeptidase I zinc metalloprotease (M18)
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 1 x MG
Ligand SD4 1 x SD4
Ligand GOL 6 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: F432
Unit cell:
a: 244.595Å b: 244.595Å c: 244.595Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.156 0.155 0.195
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Protein Assembly by Design.
Zhu et al. (2021)
1 more

7 mentions without citation

Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family.
Chaikuad et al. (2012)
6 more