Research workbench
Family 1 B-glucosidase from thermotoga maritima in complex with tetrahydrooxazine
Analyse Family 1 B-glucosidase from thermotoga maritima 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
- 1W3J
- Type
- protein
- Length
- 884 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q08638
- Ligands
- OXZ
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 443 | 45% helix, 19% strand | Q08638 |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 441 | 45% helix, 17% strand | Q08638 |
Ligands and binding sites
- OXZ · Tetrahydrooxazine · ligand · 2 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 | 751 | 0.74 | 0.79 | 59 | OXZ |
| 2 | 460 | 0.70 | 0.80 | 48 | OXZ |
| 3 | 66 | 0.35 | 0.76 | 11 | empty |
| 4 | 58 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 171 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1W3J · Family 1 b-glucosidase from Thermotoga maritima in complex with tetrahydrooxazine · 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 1W3J · PDBe 1W3J · UniProt Q08638
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