MolNFT v1 · #25912 · protein
S. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate
1W9D · Glycosidase: “S. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate”. X-ray diffraction, 8 ligands (SEH, NAG, BMA), 1 pocket (best druggability 0.74). MolNFT v1 #25912 on GenesisL1: 3D structure, binding…
- PDB
- 1W9D
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosidase
- EC
- 3.2.3.1
- Ligands
- SEH, NAG, BMA, XYP, FUC, MAN, ZN, SO4
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Glycosidase (EC 3.2.3.1) | protein | 499 | 43% helix, 18% strand | — |
Ligands and binding sites
- SEH · S-benzyl phenylacetothiohydroximate-O-sulfate · ligand · chains M
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains M
- BMA · beta-D-mannopyranose · sugar · 2 copies
- XYP · beta-D-xylopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains M
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains M
- ZN · Zinc ion · metal · chains M
- SO4 · Sulfate ion · ion · 4 copies · chains M
- GOL · Glycerol · additive · 3 copies · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.74 | 0.79 | 83 | SEH, SO4, GOL |
Modifications
Observed in the structure: 9 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 1W9D · S. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate · the same entry in another collection · chain M against M, 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
- Elsewhere: RCSB PDB 1W9D · PDBe 1W9D
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