Research workbench
Alpha-glucosidase a, agla, from thermotoga maritima in complex with maltose and NAD+
Analyse Alpha-glucosidase a, agla, from thermotoga maritima in complex with maltose and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OBB
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- EC
- 3.2.1.20
- UniProt
- O33830
- Ligands
- NAD, GLC
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase (EC 3.2.1.20) | protein | 478 | 50% helix, 15% strand | O33830 |
| B | Alpha-glucosidase (EC 3.2.1.20) | protein | 476 | 52% helix, 15% strand | O33830 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.79 | 0.85 | 76 | empty |
| 2 | 1179 | 0.76 | 0.78 | 102 | GLC, NAD |
| 3 | 1186 | 0.76 | 0.78 | 74 | GLC, NAD |
| 4 | 64 | 0.56 | 0.88 | 16 | empty |
| 5 | 171 | 0.44 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1492 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1OBB · alpha-glucosidase A, AglA, from Thermotoga maritima in complex with maltose and NAD+ · the same entry in another collection · chain A against A, TM-score 1.00
- O33830 · AlphaFold monomer V2.0 prediction for alpha-glucosidase (O33830) · 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 O33830
- Elsewhere: RCSB PDB 1OBB · PDBe 1OBB · UniProt O33830
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