Research workbench

Crystal structure of apo acid-beta-glucosidase pH 4.5

Analyse Crystal structure of apo acid-beta-glucosidase pH 4.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GXD
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, PO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glucosylceramidase (EC 3.2.1.45)	protein	497	27% helix, 28% strand	P04062

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 50 copies · chains A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	324	0.80	0.90	46	empty
2	564	0.79	0.85	65	PO4
3	205	0.76	0.91	32	PO4
4	339	0.73	0.85	38	empty
5	170	0.73	0.90	32	empty

Interfaces

5 interfaces between chains.

B–C · 1039 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 1010 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 695 Å² buried · 1 hydrogen bond · protein-protein
C–D · 621 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 279 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

3GXD · Crystal structure of Apo acid-beta-glucosidase pH 4.5 · 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 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 3GXD · PDBe 3GXD · UniProt P04062

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.