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Acid-beta-glucosidase with N-nonyl-deoxynojirimycin

Analyse Acid-beta-glucosidase with N-nonyl-deoxynojirimycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V3E
Type: protein
Length: 996 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: NND, NAG, BMA, FUC, PO4
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucosylceramidase (EC 3.2.1.45)	protein	498	28% helix, 28% strand	P04062
B	Glucosylceramidase (EC 3.2.1.45)	protein	498	28% helix, 28% strand	P04062

Ligands and binding sites

NND · (2R,3R,4R,5S)-2-(hydroxymethyl)-1-nonylpiperidine-3,4,5-triol · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
FUC · alpha-L-fucopyranose · sugar · 2 copies
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.85	0.88	58	NND
2	491	0.67	0.78	53	empty
3	385	0.67	0.80	35	empty
4	206	0.64	0.83	27	empty
5	322	0.63	0.79	48	empty

Interfaces

1 interface between chains.

A–B · 970 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

2V3E · acid-beta-glucosidase with N-nonyl-deoxynojirimycin · 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 1.00

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 2V3E · PDBe 2V3E · UniProt P04062

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