Research workbench
Crystal structure of hyperthermophilic beta-glucosidase from pyrococcus furiosus
Analyse Crystal structure of hyperthermophilic beta-glucosidase from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3APG
- Type
- protein
- Length
- 1,884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- UniProt
- Q51723
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-glucosidase | protein | 471 | 45% helix, 17% strand | Q51723 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.74 | 0.81 | 50 | GOL |
| 2 | 530 | 0.74 | 0.82 | 39 | GOL |
| 3 | 776 | 0.74 | 0.79 | 55 | GOL |
| 4 | 735 | 0.72 | 0.78 | 53 | GOL |
| 5 | 59 | 0.69 | 0.96 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1261 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1253 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1006 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 992 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3APG · Crystal structure of hyperthermophilic beta-glucosidase from pyrococcus furiosus · 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 Q51723
- Elsewhere: RCSB PDB 3APG · PDBe 3APG · UniProt Q51723
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