Research workbench
Structure of alfa-galactosidase from saccharomyces cerevisiae with raffinose
Analyse Structure of alfa-galactosidase from saccharomyces cerevisiae with raffinose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LRM
- Type
- protein
- Length
- 1,808 residues
- Chains
- 4
- 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, GLC, FRU, GLA
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 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 · 21 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.80 | 0.82 | 116 | GLC, FRU, GLA |
| 2 | 1090 | 0.80 | 0.81 | 112 | GLC, FRU, GLA |
| 3 | 1088 | 0.79 | 0.81 | 117 | GLC, FRU, GLA |
| 4 | 965 | 0.77 | 0.80 | 91 | GLC, FRU, GLA |
| 5 | 621 | 0.73 | 0.80 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1268 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1245 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1234 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1232 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 3LRM · Structure of alfa-galactosidase from Saccharomyces cerevisiae with raffinose · 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 3LRM · PDBe 3LRM · UniProt P04824
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