Research workbench
The crystal structure of the alpha-glucosidase (family 31) from ruminococcus obeum atcc 29174
Analyse The crystal structure of the alpha-glucosidase (family 31) from ruminococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N04
- Type
- protein
- Length
- 1,328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- UniProt
- A5ZY13
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-glucosidase | protein | 664 | 28% helix, 27% strand | A5ZY13 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.86 | 0.87 | 117 | empty |
| 2 | 425 | 0.75 | 0.84 | 55 | GOL |
| 3 | 465 | 0.74 | 0.83 | 59 | GOL |
| 4 | 224 | 0.67 | 0.85 | 34 | empty |
| 5 | 245 | 0.62 | 0.81 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2700 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 3N04 · THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC… · 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 A5ZY13
- Elsewhere: RCSB PDB 3N04 · PDBe 3N04 · UniProt A5ZY13
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