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Acid-beta-glucosidase low pH, glycerol bound

Analyse Acid-beta-glucosidase low pH, glycerol bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NT0
Type: protein
Length: 1,988 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucosylceramidase
EC: 3.2.1.45
UniProt: P04062
Ligands: NAG, SO4
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glucosylceramidase (EC 3.2.1.45)	protein	497	27% helix, 29% strand	P04062

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D
GOL · Glycerol · additive · 13 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1185	0.85	0.85	113	SO4, GOL
2	1152	0.85	0.85	106	SO4, GOL
3	1187	0.84	0.85	95	GOL
4	465	0.69	0.80	48	empty
5	266	0.69	0.84	38	empty

Interfaces

5 interfaces between chains.

B–C · 978 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 965 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 924 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 901 Å² buried · 1 hydrogen bond · protein-protein
B–D · 193 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2NT0 · Acid-beta-glucosidase low pH, glycerol bound · the same entry in another collection · chain D against D, TM-score 1.00
P04062 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (P04062) · a predicted model of the same protein · chain D 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 2NT0 · PDBe 2NT0 · UniProt P04062

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