MolNFT v1 · #160353 · protein
Spaga D472N structure in complex with raffinose
6PHX · Alpha-galactosidase: “Spaga D472N structure in complex with raffinose”. X-ray diffraction, 3 ligands (GLA, GLC, FRU), 8 pockets (best druggability 0.47). MolNFT v1 #160353 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6PHX
- 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, GLC, FRU
- Pockets
- 8 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 721 | 20% helix, 33% strand | A0A0H2URQ6 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 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 | 69 | 0.47 | 0.83 | 19 | GLA, GLC, FRU |
| 2 | 113 | 0.43 | 0.77 | 22 | EDO |
| 3 | 107 | 0.39 | 0.75 | 20 | empty |
| 4 | 53 | 0.36 | 0.80 | 21 | empty |
| 5 | 58 | 0.36 | 0.79 | 16 | EDO |
Compared structures
- 6PHX · SpAga D472N structure in complex with raffinose · 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 6PHX · PDBe 6PHX · UniProt A0A0H2URQ6
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