Research workbench
Aspergillus sojae alpha-glucosidase asojagdl in complex with trehalose
Analyse Aspergillus sojae alpha-glucosidase asojagdl in complex with trehalose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XOI
- Type
- protein
- Length
- 7,208 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase N-terminal polypeptide; Alpha-glucosidase C-terminal polypeptide
- EC
- 3.2.1.20
- Ligands
- NAG, GLC, BMA, NA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Alpha-glucosidase N-terminal polypeptide (EC 3.2.1.20) | protein | 465 | 19% helix, 29% strand | — |
| B, D, F, H, J, L, N, P | Alpha-glucosidase C-terminal polypeptide (EC 3.2.1.20) | protein | 436 | 24% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 89 copies · chains A, B, F, C, D, H, E, G, I, J, N, K, L, P, M, O
- GLC · alpha-D-glucopyranose · sugar · 40 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- BMA · beta-D-mannopyranose · sugar · 8 copies
- NA · Sodium ion · metal · 8 copies · chains B, D, F, H, J, L, N, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.73 | 0.80 | 78 | empty |
| 2 | 1156 | 0.73 | 0.76 | 117 | empty |
| 3 | 1051 | 0.69 | 0.74 | 123 | NAG |
| 4 | 460 | 0.63 | 0.77 | 42 | NAG |
| 5 | 228 | 0.63 | 0.82 | 39 | GLC |
Interfaces
33 interfaces between chains.
- O–P · 7669 Ų buried · 142 hydrogen bonds · protein-protein
- G–H · 7648 Ų buried · 134 hydrogen bonds · protein-protein
- C–D · 7644 Ų buried · 146 hydrogen bonds · protein-protein
- I–J · 7644 Ų buried · 146 hydrogen bonds · protein-protein
- A–B · 7644 Ų buried · 143 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 73 glycan, 24 disulfide (N-glycosylation, disulfide).
Compared structures
- 7XOI · Aspergillus sojae alpha-glucosidase AsojAgdL in complex with trehalose · 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 7XOI · PDBe 7XOI
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