Research workbench

Partially deglycosylated glucoceramidase

Analyse Partially deglycosylated glucoceramidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2J25
Type: protein
Length: 994 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucosylceramidase
EC: 3.2.1.45
UniProt: P04062
Ligands: NAG, BMA, MAN, SO4
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glucosylceramidase (EC 3.2.1.45)	protein	497	27% helix, 27% strand	P04062

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar · 2 copies
SO4 · Sulfate ion · ion · 17 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1197	0.80	0.81	93	empty
2	149	0.63	0.85	23	SO4
3	239	0.58	0.79	48	SO4
4	77	0.40	0.78	23	empty
5	53	0.29	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 566 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

2J25 · Partially deglycosylated glucoceramidase · the same entry in another collection · chain A against A, TM-score 1.00
P04062 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (P04062) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P04062
Elsewhere: RCSB PDB 2J25 · PDBe 2J25 · UniProt P04062

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