MolNFT v1 · #150497 · protein
Alpha-galactosidase from thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose
6GVD: “Alpha-galactosidase from thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose”. X-ray diffraction, 3 ligands (FDK, MG, SO4), 4 pockets (best druggability 0.69). MolNFT v1 #150497 on GenesisL1: 3D…
- PDB
- 6GVD
- Type
- protein
- Length
- 531 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- G4FEF4
- Ligands
- FDK, MG, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 531 | 28% helix, 32% strand | G4FEF4 |
Ligands and binding sites
- FDK · (1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · 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 | 472 | 0.69 | 0.80 | 53 | FDK |
| 2 | 56 | 0.32 | 0.76 | 15 | empty |
| 3 | 68 | 0.30 | 0.74 | 15 | empty |
| 4 | 53 | 0.25 | 0.73 | 22 | empty |
Compared structures
- 6GVD · Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar… · the same entry in another collection · chain A against A, TM-score 1.00
- G4FEF4 · AlphaFold monomer V2.0 prediction for alpha-galactosidase (G4FEF4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 G4FEF4
- Elsewhere: RCSB PDB 6GVD · PDBe 6GVD · UniProt G4FEF4
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