› 5kez

X-ray diffraction
1.83Å resolution

Selective and potent inhibition of the glycosidase human amylase by the short and extremely compact peptide piHA from mRNA display

Released:
DOI: 10.2210/pdb5kez/pdb
PDB entry 5kez coloured by chain, front view.
PDB entry 5kez coloured by chain, side view.
PDB entry 5kez coloured by chain, top view.
Source organisms:
Primary publication:
Rapid Discovery of Potent and Selective Glycosidase-Inhibiting De Novo Peptides.
Jongkees SAK, Caner S, Tysoe C, Brayer GD, Withers SG, Suga H
Cell Chem Biol 24 381-390 (2017)
PMID: 28262556

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138164 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pancreatic alpha-amylase Chain: A
Molecule details ›
Chain: A
Length: 496 amino acids
Theoretical weight: 55.93 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P04746 (Residues: 16-511; Coverage: 100%)
Gene name: AMY2A
Sequence domains:
Structure domains:
ACE-DTY-PRO-TYR-SER-CYS-TRP-VAL-ARG-HIS-NH2 Chain: B
Molecule details ›
Chain: B
Length: 11 amino acids
Theoretical weight: 1.24 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand CA 1 x CA
2 modified residues:
Ligand PCA 1 x PCA
Ligand DTY 1 x DTY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 52.8Å b: 75.84Å c: 137.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.208
Expression systems:
  • Komagataella pastoris
  • Not provided

Quick links

Citations

6 review citations

Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads.
Obexer et al. (2017)
5 more

3 mentions without citation

Structural Features and Binding Modes of Thioether-Cyclized Peptide Ligands.
Otero-Ramirez et al. (2018)
2 more