MolNFT v1 · #53527 · protein
A micromolar O-sulfated thiohydroximate inhibitor bound to plant myrosinase
2WXD: “A micromolar O-sulfated thiohydroximate inhibitor bound to plant myrosinase”. X-ray diffraction, 8 ligands (E18, NAG, BMA), 2 pockets (best druggability 0.74). MolNFT v1 #53527 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2WXD
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myrosinase
- EC
- 3.2.3.1
- UniProt
- P29736
- Ligands
- E18, NAG, BMA, XYP, FUC, MAN, ZN, SO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Myrosinase (EC 3.2.3.1) | protein | 499 | 43% helix, 17% strand | P29736 |
Ligands and binding sites
- E18 · 2-(dimethylamino)ethyl (1Z)-2-phenyl-N-(sulfooxy)ethanimidothioate · ligand · chains M
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 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
- ZN · Zinc ion · metal · chains M
- SO4 · Sulfate ion · ion · 7 copies · chains M
- GOL · Glycerol · additive · 4 copies · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.74 | 0.81 | 47 | E18, SO4 |
| 2 | 91 | 0.36 | 0.75 | 26 | empty |
Modifications
Observed in the structure: 10 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 2WXD · A micromolar O-sulfated thiohydroximate inhibitor bound to plant myrosinase · the same entry in another collection · chain M against M, TM-score 1.00
- P29736 · AlphaFold monomer V2.0 prediction for myrosinase MA1 (P29736) · a predicted model of the same protein · chain M 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 P29736
- Elsewhere: RCSB PDB 2WXD · PDBe 2WXD · UniProt P29736
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