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Crystal structure of N370S glucocerebrosidase mutant at pH 7.4
Analyse Crystal structure of N370S glucocerebrosidase mutant at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KEH
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocerebrosidase
- EC
- 3.2.1.45
- UniProt
- P04062
- Ligands
- NAG, NDG, SO4
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucocerebrosidase (EC 3.2.1.45) | protein | 497 | 27% helix, 30% strand | P04062 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.63 | 0.78 | 50 | GOL |
| 2 | 121 | 0.50 | 0.80 | 22 | GOL |
| 3 | 119 | 0.48 | 0.79 | 28 | empty |
| 4 | 112 | 0.47 | 0.79 | 26 | empty |
| 5 | 86 | 0.42 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3KEH · Crystal Structure of N370S Glucocerebrosidase mutant at pH 7.4 · 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 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 3KEH · PDBe 3KEH · UniProt P04062
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