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Crystal structure of thermoanaerobacterium xylanolyticum GH116 beta- glucosidase with 2-deoxy-2-fluoroglucoside
Analyse Crystal structure of thermoanaerobacterium xylanolyticum GH116 beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BX2
- Type
- protein
- Length
- 769 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- F6BL85
- Ligands
- G2F, CA
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 769 | 31% helix, 23% strand | F6BL85 |
Ligands and binding sites
- G2F · 2-deoxy-2-fluoro-alpha-D-glucopyranose · ligand · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 17 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.50 | 0.77 | 27 | G2F, GOL |
| 2 | 130 | 0.43 | 0.76 | 23 | empty |
| 3 | 87 | 0.37 | 0.76 | 23 | empty |
| 4 | 71 | 0.36 | 0.77 | 14 | GOL |
| 5 | 57 | 0.29 | 0.75 | 15 | GOL |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5BX2 · Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase 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 5BX2 · PDBe 5BX2 · UniProt F6BL85
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