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X-ray structure of acarbose bound to amylomaltase from thermus aquaticus. implications for the synthesis of large cyclic glucans
Analyse X-ray structure of acarbose bound to amylomaltase from thermus aquaticus.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ESW
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amylomaltase
- EC
- 2.4.1.25
- UniProt
- O87172
- Ligands
- AC1, GLC
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amylomaltase (EC 2.4.1.25) | protein | 500 | 46% helix, 12% strand | O87172 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.79 | 0.98 | 30 | empty |
| 2 | 737 | 0.69 | 0.76 | 62 | GLC, AC1, EDO |
| 3 | 168 | 0.46 | 0.75 | 25 | GLC, EDO |
| 4 | 89 | 0.42 | 0.78 | 22 | empty |
| 5 | 80 | 0.38 | 0.77 | 17 | empty |
Compared structures
- 1ESW · X-ray structure of acarbose bound to amylomaltase from thermus aquaticus. implications… · the same entry in another collection · chain A against A, TM-score 1.00
- O87172 · AlphaFold monomer V2.0 prediction for 4-alpha-glucanotransferase (O87172) · a predicted model of the same protein · 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 O87172
- Elsewhere: RCSB PDB 1ESW · PDBe 1ESW · UniProt O87172
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