Research workbench
Amylase in complex with acarbose
Analyse Amylase in complex with acarbose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GXV
- Type
- protein
- Length
- 962 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.07
- Source
- Alicyclobacillus sp.
- Molecule
- A-amylase
- UniProt
- A0A3P8MUS3
- Ligands
- GLC, AC1, BGC, CA, NA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.07 · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | A-amylase | protein | 481 | 28% helix, 26% strand | A0A3P8MUS3 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.80 | 0.82 | 69 | GLC, AC1, BGC |
| 2 | 823 | 0.74 | 0.78 | 57 | GLC, AC1, BGC |
| 3 | 228 | 0.50 | 0.75 | 32 | empty |
| 4 | 76 | 0.42 | 0.80 | 21 | empty |
| 5 | 59 | 0.35 | 0.78 | 14 | AC1 |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6GXV · Amylase in complex with acarbose · 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 A0A3P8MUS3
- Elsewhere: RCSB PDB 6GXV · PDBe 6GXV · UniProt A0A3P8MUS3
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