Research workbench
Taka-amylase
Analyse Taka-amylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YQ7
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.58
- Source
- Aspergillus oryzae
- Molecule
- Alpha-amylase
- EC
- 3.2.1.1
- UniProt
- A0A1S9DH83
- Ligands
- NAG, CA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.58 · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 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 A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.61 | 0.78 | 29 | empty |
| 2 | 332 | 0.61 | 0.78 | 25 | EDO |
| 3 | 293 | 0.58 | 0.78 | 55 | empty |
| 4 | 328 | 0.55 | 0.75 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 634 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6YQ7 · Taka-amylase · the same entry in another collection · chain A against A, TM-score 1.00
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 6YQ7 · PDBe 6YQ7 · UniProt A0A1S9DH83
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.