Research workbench
Crystal structure of the GH1 beta-glucosidase from exiguobacterium antarcticum B7 in space group C2221
Analyse Crystal structure of the GH1 beta-glucosidase from exiguobacterium antarcticum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DT7
- Type
- protein
- Length
- 1,776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- K0A8J9
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 444 | 45% helix, 17% strand | K0A8J9 |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 442 | 44% helix, 16% strand | K0A8J9 |
| C, D | Beta-glucosidase (EC 3.2.1.21) | protein | 445 | 44% helix, 17% strand | K0A8J9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.80 | 0.81 | 104 | CXS |
| 2 | 425 | 0.70 | 0.81 | 45 | empty |
| 3 | 458 | 0.69 | 0.80 | 48 | CXS |
| 4 | 79 | 0.32 | 0.74 | 25 | GOL |
| 5 | 62 | 0.30 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- C–D · 881 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 625 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DT7 · Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in… · 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 K0A8J9
- Elsewhere: RCSB PDB 5DT7 · PDBe 5DT7 · UniProt K0A8J9
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