MolNFT v1 · #17044 · protein

Human acid-beta-glucosidase

1OGS · Glucosylceramidase: “Human acid-beta-glucosidase”. X-ray diffraction, 2 ligands (NAG, SO4), 7 pockets (best druggability 0.62). MolNFT v1 #17044 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1OGS
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, 2.4.1.-, 3.2.1.104
UniProt: P04062
Ligands: NAG, SO4
Pockets: 7 · best druggability 0.62

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glucosylceramidase (EC 3.2.1.45, 2.4.1.-, 3.2.1.104)	protein	497	27% helix, 29% strand	P04062

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
SO4 · Sulfate ion · ion · 15 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.62	0.85	27	empty
2	252	0.60	0.80	47	empty
3	297	0.59	0.78	36	SO4
4	233	0.55	0.78	37	empty
5	81	0.35	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 398 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1OGS · human acid-beta-glucosidase · 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 B 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 1OGS · PDBe 1OGS · UniProt P04062

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