MolNFT v1 · #91793 · protein
Crystal structure of GH36 alpha-galactosidase agaa A355E D548N from geobacillus stearothermophilus in complex with raffinose
4FNT: “Crystal structure of GH36 alpha-galactosidase agaa A355E D548N from geobacillus stearothermophilus in complex…”. X-ray diffraction, 3 ligands (FRU, GLC, GLA), 20 pockets (best druggability 0.84). MolNFT v1 #91793 on GenesisL1: 3D…
- PDB
- 4FNT
- Type
- protein
- Length
- 2,872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase agaa
- EC
- 3.2.1.22
- UniProt
- Q9ALJ4
- Ligands
- FRU, GLC, GLA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-galactosidase agaa (EC 3.2.1.22) | protein | 718 | 21% helix, 33% strand | Q9ALJ4 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains B, C, A, D
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B, C, A, D
- GLA · alpha-D-galactopyranose · sugar · 3 copies · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.84 | 103 | empty |
| 2 | 1139 | 0.83 | 0.84 | 122 | empty |
| 3 | 877 | 0.83 | 0.85 | 96 | empty |
| 4 | 702 | 0.83 | 0.87 | 60 | empty |
| 5 | 1021 | 0.83 | 0.84 | 109 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3373 Ų buried · 74 hydrogen bonds · protein-protein
- A–D · 3304 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 1931 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1911 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4FNT · Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9ALJ4 · AlphaFold monomer V2.0 prediction for alpha-galactosidase agaa (Q9ALJ4) · a predicted model of the same protein · chain D 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 Q9ALJ4
- Elsewhere: RCSB PDB 4FNT · PDBe 4FNT · UniProt Q9ALJ4
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