Research workbench
Crystal structure of recombinant human beta-glucocerebrosidase in complex with biphenyl-cyclophellitol inhibitor (ME655)
Analyse Crystal structure of recombinant human beta-glucocerebrosidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q6N
- Type
- protein
- Length
- 986 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- P04062
- Ligands
- HK2, NAG, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 496 | 28% helix, 27% strand | P04062 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 490 | 28% helix, 29% strand | P04062 |
Ligands and binding sites
- HK2 · (1~{S},3~{S},4~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-[[4-[3-(4-phenylphenoxy)propyl]-1,2,3-triazol-1-yl]methyl]cyclohexan-1-olate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 15 copies · chains A, B
- ACT · Acetate ion · additive · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.71 | 0.78 | 69 | SO4, HK2, ACT |
| 2 | 345 | 0.62 | 0.78 | 43 | HK2, ACT |
| 3 | 148 | 0.53 | 0.80 | 26 | ACT |
| 4 | 120 | 0.48 | 0.79 | 30 | empty |
| 5 | 129 | 0.46 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 461 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6Q6N · Crystal structure of recombinant human beta-glucocerebrosidase in complex with… · 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 6Q6N · PDBe 6Q6N · UniProt P04062
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