Research workbench
Beta-glucosidase from thermotoga maritima in complex with gluco-1H- imidazole
Analyse Beta-glucosidase from thermotoga maritima in complex with gluco-1H- imidazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OSS
- Type
- protein
- Length
- 886 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase a
- EC
- 3.2.1.21
- UniProt
- Q08638
- Ligands
- AEZ, NA, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase a (EC 3.2.1.21) | protein | 443 | 45% helix, 19% strand | Q08638 |
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 B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.73 | 0.79 | 60 | EDO |
| 2 | 486 | 0.71 | 0.80 | 43 | EDO, AEZ |
| 3 | 80 | 0.37 | 0.76 | 12 | empty |
| 4 | 59 | 0.35 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5OSS · Beta-glucosidase from Thermotoga maritima in complex with Gluco-1H-imidazole · the same entry in another collection · chain A against A, TM-score 1.00
- Q08638 · AlphaFold monomer V2.0 prediction for beta-glucosidase a (Q08638) · 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 Q08638
- Elsewhere: RCSB PDB 5OSS · PDBe 5OSS · UniProt Q08638
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