MolNFT v1 · #160354 · protein
Spaga D472N structure in complex alpha 1,3 galactobiose
6PHY · Alpha-galactosidase: “Spaga D472N structure in complex alpha 1,3 galactobiose”. X-ray diffraction, 2 ligands (GLA, GAL), 8 pockets (best druggability 0.48). MolNFT v1 #160354 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6PHY
- Type
- protein
- Length
- 721 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- A0A0H2URQ6
- Ligands
- GLA, GAL
- Pockets
- 8 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 721 | 21% helix, 33% strand | A0A0H2URQ6 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 3 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.48 | 0.79 | 27 | GAL, GLA |
| 2 | 122 | 0.44 | 0.77 | 22 | empty |
| 3 | 119 | 0.39 | 0.75 | 21 | EDO |
| 4 | 52 | 0.38 | 0.80 | 18 | empty |
| 5 | 56 | 0.36 | 0.79 | 16 | EDO |
Compared structures
- 6PHY · SpAga D472N structure in complex alpha 1,3 galactobiose · the same entry in another collection · 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 A0A0H2URQ6
- Elsewhere: RCSB PDB 6PHY · PDBe 6PHY · UniProt A0A0H2URQ6
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