Research workbench
Glucocerebrosidase in complex with pharmacological chaperone IMX8
Analyse Glucocerebrosidase in complex with pharmacological chaperone IMX8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q1N
- Type
- protein
- Length
- 983 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- B2R6A7
- Ligands
- P9V, NAG, FUC, MAN, SO4
- Pockets
- 6 · 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 | 489 | 28% helix, 28% strand | B2R6A7 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 494 | 28% helix, 28% strand | B2R6A7 |
Ligands and binding sites
- P9V · (2R,3S,4S,5R)-2-[2-(methylsulfanyl)ethyl]piperidine-3, 4,5-triol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 17 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.71 | 0.77 | 80 | SO4, P9V |
| 2 | 300 | 0.65 | 0.81 | 46 | EDO, SO4 |
| 3 | 278 | 0.58 | 0.78 | 47 | EDO, SO4 |
| 4 | 132 | 0.48 | 0.78 | 25 | P9V |
| 5 | 71 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6Q1N · Glucocerebrosidase in complex with pharmacological chaperone IMX8 · the same entry in another collection · chain A 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 B2R6A7
- Elsewhere: RCSB PDB 6Q1N · PDBe 6Q1N · UniProt B2R6A7
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