› 6yq9

X-ray diffraction
1.55Å resolution

Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor

Released:
DOI: 10.2210/pdb6yq9/pdb
PDB entry 6yq9 coloured by chain, front view.
PDB entry 6yq9 coloured by chain, side view.
PDB entry 6yq9 coloured by chain, top view.
Source organism: Aspergillus oryzae
Primary publication:
Activity-Based Protein Profiling of Retaining α-Amylases in Complex Biological Samples.
Chen Y, Armstrong Z, Artola M, Florea BI, Kuo CL, de Boer C, Rasmussen MS, Abou Hachem M, van der Marel GA, Codée JDC, Aerts JMFG, Davies GJ, Overkleeft HS
OpenAccess logo J Am Chem Soc 143 2423-2432 (2021)
PMID: 33497208

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-103740 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-amylase Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
Length: 499 amino acids
Theoretical weight: 54.85 KDa
Source organism: Aspergillus oryzae
Expression system: Aspergillus oryzae
UniProt:
  • Canonical: A0A1S9DH83 (Residues: 1-499; Coverage: 100%)
Gene name: OAory_01097160
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand NAG 2 x NAG
Ligand EDO 4 x EDO
Ligand 5QP 2 x 5QP
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 65.214Å b: 103.1Å c: 75.374Å
α: 90° β: 103.632° γ: 90°
R-values:
R R work R free
0.148 0.146 0.174
Expression system: Aspergillus oryzae

Quick links

Citations

2 review citations

Recent advances in activity-based probes (ABPs) and affinity-based probes (AfBPs) for profiling of enzymes.
Fang et al. (2021)
1 more

1 mention without citation

Activity-Based Protein Profiling of Retaining α-Amylases in Complex Biological Samples.
Chen et al. (2021)