Research workbench
Structure of alfa-galactosidase (MEL1) from saccharomyces cerevisiae
Analyse Structure of alfa-galactosidase (MEL1) from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LRK
- Type
- protein
- Length
- 452 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase 1
- EC
- 3.2.1.22
- UniProt
- P04824
- Ligands
- NAG, NA
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase 1 (EC 3.2.1.22) | protein | 452 | 29% helix, 22% strand | P04824 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.52 | 0.79 | 27 | GOL |
| 2 | 184 | 0.48 | 0.76 | 24 | empty |
| 3 | 92 | 0.45 | 0.80 | 24 | empty |
| 4 | 50 | 0.44 | 0.84 | 15 | GOL |
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3LRK · Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P04824 · AlphaFold monomer V2.0 prediction for alpha-galactosidase 1 (P04824) · 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 P04824
- Elsewhere: RCSB PDB 3LRK · PDBe 3LRK · UniProt P04824
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