› 3fvy

X-ray diffraction
1.9Å resolution

Crystal structure of human Dipeptidyl Peptidase III

Released:
DOI: 10.2210/pdb3fvy/pdb
PDB entry 3fvy coloured by chain, front view.
PDB entry 3fvy coloured by chain, side view.
PDB entry 3fvy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III.
Bezerra GA, Dobrovetsky E, Viertlmayr R, Dong A, Binter A, Abramic M, Macheroux P, Dhe-Paganon S, Gruber K
Proc Natl Acad Sci U S A 109 6525-30 (2012)
PMID: 22493238

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide from a peptide comprising four or more residues, with broad specificity. Also acts on dipeptidyl 2-naphthylamides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192691 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidyl peptidase 3 Chain: A
Molecule details ›
Chain: A
Length: 728 amino acids
Theoretical weight: 81.77 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NY33 (Residues: 1-726; Coverage: 99%)
Gene name: DPP3
Sequence domains: Peptidase family M49
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 2 x MG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 49.812Å b: 151.378Å c: 53.721Å
α: 90° β: 100.04° γ: 90°
R-values:
R R work R free
0.172 0.172 0.219
Expression system: Spodoptera frugiperda

Quick links

Citations

3 review citations

Endogenous opiates and behavior: 2012.
Bodnar RJ. (2013)
2 more

19 mentions without citation

Benefits of structural genomics for drug discovery research.
Grabowski et al. (2009)
18 more