Research workbench
Crystal structure of bacterial glucoamylase complexed with acarbose
Analyse Crystal structure of bacterial glucoamylase complexed with acarbose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LF9
- Type
- protein
- Length
- 1,348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucoamylase
- EC
- 3.2.1.3
- Ligands
- AC1, GLC, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucoamylase (EC 3.2.1.3) | protein | 674 | 34% helix, 23% strand | — |
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, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.81 | 0.84 | 101 | GLC, AC1, SO4 |
| 2 | 186 | 0.64 | 0.84 | 30 | GLC, AC1 |
| 3 | 115 | 0.44 | 0.78 | 26 | empty |
| 4 | 118 | 0.43 | 0.77 | 29 | empty |
| 5 | 64 | 0.42 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 549 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1LF9 · Crystal structure of bacterial glucoamylase complexed 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
- Elsewhere: RCSB PDB 1LF9 · PDBe 1LF9
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