GL1X · GenesisL1 explorer

MolNFT v1 · #121867 · protein

Asmase with zinc

5I81 · Sphingomyelin phosphodiesterase: “Asmase with zinc”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 3 pockets (best druggability 0.59). MolNFT v1 #121867 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5I81
Type
protein
Length
528 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Sphingomyelin phosphodiesterase
EC
3.1.4.12
UniProt
P17405
Ligands
NAG, BMA, MAN, ZN, SO4
Pockets
3 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ASphingomyelin phosphodiesterase (EC 3.1.4.12)protein52839% helix, 15% strandP17405

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
  • BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
  • MAN · alpha-D-mannopyranose · sugar
  • ZN · Zinc ion · metal · 2 copies · chains A
  • SO4 · Sulfate ion · ion · 11 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11720.590.8238empty
21450.410.7325empty
31030.360.7421SO4

Modifications

Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

  • 5I81 · aSMase with zinc · the same entry in another collection · chain A against A, TM-score 1.00
  • P17405 · AlphaFold monomer V2.0 prediction for sphingomyelin phosphodiesterase (P17405) · a predicted model of the same protein · chain A against A, TM-score 1.00

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