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Crystal structure of acid-beta-glucosidase at pH 5.5

Analyse Crystal structure of acid-beta-glucosidase at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GXI
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: 19 · best druggability 0.86

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	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 · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 63 copies · chains A, B, D, C

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

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	848	0.86	0.88	92	PO4
2	590	0.84	0.88	68	empty
3	536	0.82	0.87	71	empty
4	313	0.67	0.82	43	empty
5	375	0.65	0.79	42	empty

Interfaces

5 interfaces between chains.

B–C · 1014 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 1005 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 719 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 693 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 229 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3GXI · Crystal structure of acid-beta-glucosidase at pH 5.5 · the same entry in another collection · chain B against B, 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 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 3GXI · PDBe 3GXI · UniProt P04062

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