MolNFT v1 · #75135 · protein
The crystal structure of the W169Y mutant of alpha-glucosidase (GH31 family) from ruminococcus obeum atcc 29174 in complex with acarbose
3PHA: “The crystal structure of the W169Y mutant of alpha-glucosidase (GH31 family) from ruminococcus obeum atcc…”. X-ray diffraction, 2 ligands (AC1, GLC), 20 pockets (best druggability 0.87). MolNFT v1 #75135 on GenesisL1: 3D structure…
- PDB
- 3PHA
- Type
- protein
- Length
- 2,660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- EC
- 3.2.1.-
- UniProt
- A5ZY13
- Ligands
- AC1, GLC
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase (EC 3.2.1.-) | protein | 664 | 27% helix, 25% strand | A5ZY13 |
| B, C | Alpha-glucosidase (EC 3.2.1.-) | protein | 665 | 28% helix, 26% strand | A5ZY13 |
| D | Alpha-glucosidase (EC 3.2.1.-) | protein | 666 | 27% helix, 26% strand | A5ZY13 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.87 | 0.88 | 113 | empty |
| 2 | 408 | 0.85 | 0.93 | 44 | empty |
| 3 | 539 | 0.81 | 0.87 | 65 | empty |
| 4 | 687 | 0.72 | 0.79 | 68 | empty |
| 5 | 566 | 0.67 | 0.77 | 70 | GLC, AC1 |
Interfaces
5 interfaces between chains.
- C–D · 2796 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2787 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PHA · The crystal structure of the W169Y mutant of alpha-glucosidase (gh31 family) from… · 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 3PHA · PDBe 3PHA · UniProt A5ZY13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.