Research workbench
Bombyx mori GH13 sucrose hydrolase complexed with acarbose
Analyse Bombyx mori GH13 sucrose hydrolase 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
- 6LGE
- Type
- protein
- Length
- 1,139 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose hydrolase
- UniProt
- A0A077JI83
- Ligands
- AC1, BGC, GLC, MG, CA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sucrose hydrolase | protein | 570 | 29% helix, 19% strand | A0A077JI83 |
| B | Sucrose hydrolase | protein | 569 | 29% helix, 19% strand | A0A077JI83 |
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
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.77 | 0.80 | 73 | MG |
| 2 | 362 | 0.65 | 0.79 | 48 | BGC, GLC, AC1 |
| 3 | 322 | 0.62 | 0.79 | 43 | BGC, GLC, AC1, MG |
| 4 | 324 | 0.54 | 0.74 | 43 | empty |
| 5 | 279 | 0.51 | 0.74 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1194 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6LGE · Bombyx mori GH13 sucrose hydrolase 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
- Every structure of UniProt A0A077JI83
- Elsewhere: RCSB PDB 6LGE · PDBe 6LGE · UniProt A0A077JI83
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