Research workbench
Structural analysis of a beta-glucosidase mutant derived from a hyperthermophilic tetrameric structure
Analyse Structural analysis of a beta-glucosidase mutant derived from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WDP
- Type
- protein
- Length
- 1,888 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q51723
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, Q, R, S | Beta-glucosidase (EC 3.2.1.21) | protein | 472 | 46% helix, 17% strand | Q51723 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains P, Q, R, S
- GOL · Glycerol · additive · 11 copies · chains P, Q, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.71 | 0.80 | 47 | GOL, PO4 |
| 2 | 524 | 0.71 | 0.80 | 46 | GOL |
| 3 | 550 | 0.71 | 0.79 | 44 | GOL, PO4 |
| 4 | 547 | 0.71 | 0.79 | 46 | GOL, PO4 |
| 5 | 308 | 0.65 | 0.81 | 48 | empty |
Interfaces
3 interfaces between chains.
- P–Q · 1188 Ų buried · 6 hydrogen bonds · protein-protein
- R–S · 956 Ų buried · 5 hydrogen bonds · protein-protein
- Q–R · 870 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3WDP · Structural analysis of a beta-glucosidase mutant derived from a hyperthermophilic… · the same entry in another collection · chain P against P, 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 Q51723
- Elsewhere: RCSB PDB 3WDP · PDBe 3WDP · UniProt Q51723
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