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Crystal structure of susg with acarbose
Analyse Crystal structure of susg with acarbose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K8M
- Type
- protein
- Length
- 1,296 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, susg
- UniProt
- Q8A1G3
- Ligands
- AC1, GLC, CA
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase, susg | protein | 650 | 27% helix, 23% strand | Q8A1G3 |
| B | Alpha-amylase, susg | protein | 646 | 25% helix, 24% strand | Q8A1G3 |
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 · 6 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 14 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.62 | 0.75 | 52 | empty |
| 2 | 157 | 0.45 | 0.75 | 20 | GLC, AC1 |
| 3 | 143 | 0.43 | 0.75 | 20 | GLC, AC1 |
| 4 | 140 | 0.42 | 0.75 | 31 | empty |
| 5 | 85 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 162 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 2 glycan (engineered, glycosylation).
Compared structures
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 Q8A1G3
- Elsewhere: RCSB PDB 3K8M · PDBe 3K8M · UniProt Q8A1G3
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