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Asmase with zinc and phosphocholine

Analyse Asmase with zinc and phosphocholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5I85
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
PC, NAG, BMA, MAN, ZN, SO4
Pockets
2 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ASphingomyelin phosphodiesterase (EC 3.1.4.12)protein52839% helix, 14% strandP17405

Ligands and binding sites

  • PC · Phosphocholine · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
  • BMA · beta-D-mannopyranose · sugar · 2 copies
  • MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
  • 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

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11580.610.8434empty
22180.460.7340PC

Modifications

Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

  • 5I85 · aSMase with zinc and phosphocholine · 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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