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The crystal structure of the alpha-glucosidase (gh 31) from ruminococcus obeum atcc 29174 in complex with voglibose
Analyse The crystal structure of the alpha-glucosidase (gh 31) from ruminococcus obeum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C9X
- Type
- protein
- Length
- 1,330 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
- VOG, K, CL
- Pockets
- 14 · 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 | 666 | 28% helix, 25% strand | A5ZY13 |
| B | Glycosyl hydrolase, family 31 (EC 3.2.1.-) | protein | 664 | 28% helix, 26% strand | A5ZY13 |
Ligands and binding sites
- VOG · (1S,2S,3R,4S,5S)-5-[(1,3-dihydroxypropan-2-yl)amino]-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.87 | 0.89 | 105 | empty |
| 2 | 482 | 0.65 | 0.77 | 64 | VOG |
| 3 | 277 | 0.60 | 0.80 | 32 | GOL |
| 4 | 365 | 0.59 | 0.76 | 44 | VOG |
| 5 | 100 | 0.58 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2641 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 6C9X · THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (GH 31) FROM RUMINOCOCCUS OBEUM ATCC 29174… · 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 6C9X · PDBe 6C9X · UniProt A5ZY13
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