Research workbench
Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator
Analyse Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LVX
- Type
- protein
- Length
- 1,987 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
- 79B, 7E4, NAG, MAN, BMA, PO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 27% helix, 27% strand | P04062 |
| C | Glucosylceramidase (EC 3.2.1.45) | protein | 496 | 27% helix, 28% strand | P04062 |
Ligands and binding sites
- 79B · 11-[(2~{R})-2-[(2-pyridin-3-ylquinazolin-4-yl)amino]-2, 3-dihydro-1~{H}-inden-5-yl]undec-10-ynoic acid · ligand · 2 copies · chains A, B, C, D
- 7E4 · 11-[(2~{S})-2-[(2-pyridin-3-ylquinazolin-4-yl)amino]-2, 3-dihydro-1~{H}-inden-5-yl]undec-10-ynoic acid · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- PO4 · Phosphate ion · ion · 21 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.81 | 0.82 | 90 | 79B, 7E4 |
| 2 | 873 | 0.80 | 0.82 | 86 | 7E4, 79B |
| 3 | 775 | 0.79 | 0.82 | 89 | PO4 |
| 4 | 765 | 0.78 | 0.82 | 66 | empty |
| 5 | 781 | 0.74 | 0.79 | 81 | empty |
Interfaces
6 interfaces between chains.
- B–C · 633 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 407 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 398 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 197 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan, 4 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5LVX · Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator · 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 C 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 5LVX · PDBe 5LVX · UniProt P04062
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