Research workbench
The crystal structure of the W169Y mutant of alpha-glucosidase (gh 31) from ruminococcus obeum atcc 29174 in complex with miglitol
Analyse The crystal structure of the W169Y mutant of alpha-glucosidase (gh 31) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CA1
- Type
- protein
- Length
- 1,329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase, family 31
- EC
- 3.2.1.-
- UniProt
- A5ZY13
- Ligands
- MIG
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase, family 31 (EC 3.2.1.-) | protein | 664 | 28% helix, 26% strand | A5ZY13 |
| B | Glycosyl hydrolase, family 31 (EC 3.2.1.-) | protein | 665 | 28% helix, 26% strand | A5ZY13 |
Ligands and binding sites
- MIG · (2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl) piperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.87 | 0.90 | 88 | empty |
| 2 | 581 | 0.66 | 0.76 | 63 | MIG |
| 3 | 251 | 0.62 | 0.81 | 31 | GOL |
| 4 | 288 | 0.60 | 0.78 | 32 | MIG |
| 5 | 236 | 0.58 | 0.80 | 30 | GOL |
Interfaces
1 interface between chains.
- A–B · 2794 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6CA1 · THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (GH 31) FROM RUMINOCOCCUS… · 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 6CA1 · PDBe 6CA1 · UniProt A5ZY13
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