Research workbench
Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor
Analyse Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YQ9
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Aspergillus oryzae
- Molecule
- Alpha-amylase
- EC
- 3.2.1.1
- UniProt
- A0A1S9DH83
- Ligands
- NAG, 5QP, CA
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.55 · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA, BBB | Alpha-amylase (EC 3.2.1.1) | protein | 476 | 36% helix, 21% strand | A0A1S9DH83 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains AAA, BBB
- 5QP · (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside · sugar · 2 copies · chains AAA, BBB
- CA · Calcium ion · metal · 2 copies · chains AAA, BBB
- EDO · 1,2-ethanediol · additive · 4 copies · chains AAA, BBB
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.61 | 0.78 | 27 | 5QP |
| 2 | 279 | 0.60 | 0.79 | 45 | empty |
| 3 | 312 | 0.60 | 0.78 | 27 | 5QP |
| 4 | 242 | 0.52 | 0.76 | 40 | empty |
| 5 | 89 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- AAA–BBB · 574 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation, glycosylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A1S9DH83
- Elsewhere: RCSB PDB 6YQ9 · PDBe 6YQ9 · UniProt A0A1S9DH83
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