MolNFT v1 · #117223 · protein
Mutant (D415G) GH97 alpha-galactosidase in complex with gal-lac
5E1Q · Retaining alpha-galactosidase: “Mutant (D415G) GH97 alpha-galactosidase in complex with gal-lac”. X-ray diffraction, 4 ligands (BGC, GLA, GAL), 9 pockets (best druggability 0.58). MolNFT v1 #117223 on GenesisL1: 3D structure…
- PDB
- 5E1Q
- Type
- protein
- Length
- 1,286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retaining alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- Q8A6L0
- Ligands
- BGC, GLA, GAL, CA
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retaining alpha-galactosidase (EC 3.2.1.22) | protein | 642 | 19% helix, 38% strand | Q8A6L0 |
| B | Retaining alpha-galactosidase (EC 3.2.1.22) | protein | 644 | 19% helix, 38% strand | Q8A6L0 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.58 | 0.75 | 66 | empty |
| 2 | 247 | 0.55 | 0.77 | 39 | empty |
| 3 | 125 | 0.55 | 0.83 | 25 | BGC, GLA, CA |
| 4 | 256 | 0.55 | 0.77 | 39 | GOL |
| 5 | 127 | 0.52 | 0.81 | 25 | BGC, GLA, CA |
Interfaces
1 interface between chains.
- A–B · 264 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5E1Q · Mutant (D415G) GH97 alpha-galactosidase in complex with Gal-Lac · the same entry in another collection · chain A against A, TM-score 1.00
- Q8A6L0 · AlphaFold monomer V2.0 prediction for retaining alpha-galactosidase (Q8A6L0) · 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 Q8A6L0
- Elsewhere: RCSB PDB 5E1Q · PDBe 5E1Q · UniProt Q8A6L0
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