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Crystal structure of human cytosolic neutral beta-glycosylceramidase (klotho-related PROTE:KLRP) complex with glucose and fatty acids

Analyse Crystal structure of human cytosolic neutral beta-glycosylceramidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2E9L
Type
protein
Length
466 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cytosolic beta-glucosidase
EC
3.2.1.21
UniProt
Q9H227
Ligands
PLM, OLA, BGC
Pockets
1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACytosolic beta-glucosidase (EC 3.2.1.21)protein46645% helix, 18% strandQ9H227

Ligands and binding sites

  • PLM · Palmitic acid · ligand · 2 copies · chains A
  • OLA · Oleic acid · ligand · chains A
  • BGC · beta-D-glucopyranose · sugar · chains A
  • GOL · Glycerol · additive · 3 copies · chains A

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
15910.780.8345BGC, PLM, OLA

Compared structures

  • 2E9L · Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9H227 · AlphaFold monomer V2.0 prediction for cytosolic beta-glucosidase (Q9H227) · a predicted model of the same protein · chain A against A, TM-score 1.00

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