Research workbench
Beta-glucosidase from thermoanaerobacterium xylolyticum GH116 in complex with gluco-1H-imidazole
Analyse Beta-glucosidase from thermoanaerobacterium xylolyticum GH116 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
- 5OST
- Type
- protein
- Length
- 762 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- F6BL85
- Ligands
- AEZ, CA, CL
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 762 | 31% helix, 23% strand | F6BL85 |
Ligands and binding sites
- AEZ · (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.53 | 0.81 | 25 | AEZ |
| 2 | 90 | 0.36 | 0.75 | 19 | EDO |
| 3 | 68 | 0.33 | 0.76 | 15 | empty |
| 4 | 70 | 0.33 | 0.75 | 19 | empty |
| 5 | 73 | 0.31 | 0.74 | 17 | EDO |
Compared structures
- 5OST · Beta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in complex with… · 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 F6BL85
- Elsewhere: RCSB PDB 5OST · PDBe 5OST · UniProt F6BL85
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