GL1X · GenesisL1 explorer

MolNFT v1 · #25910 · protein

S. alba myrosinase in complex with carba-glucotropaeolin

1W9B · Glycosidase: “S. alba myrosinase in complex with carba-glucotropaeolin”. X-ray diffraction, 8 ligands (CGT, NAG, BMA), 1 pocket (best druggability 0.75). MolNFT v1 #25910 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1W9B
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
CGT, NAG, BMA, XYP, FUC, MAN, ZN, SO4
Pockets
1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
MGlycosidase (EC 3.2.3.1)protein49943% helix, 18% strand—

Ligands and binding sites

  • CGT · Carba-glucotropaeolin · 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17740.750.8080CGT, GOL, SO4

Modifications

Observed in the structure: 9 glycan, 3 disulfide (N-glycosylation, disulfide).

Compared structures

  • 1W9B · S. alba myrosinase in complex with carba-glucotropaeolin · the same entry in another collection · chain M against M, TM-score 1.00

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