Research workbench
Family 1 6-phospho-beta-D glycosidase from streptococcus pyogenes
Analyse Family 1 6-phospho-beta-D glycosidase from streptococcus pyogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B3K
- Type
- protein
- Length
- 2,766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21, 3.2.1.86
- UniProt
- Q99YP9
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-glucosidase (EC 3.2.1.21, 3.2.1.86) | protein | 461 | 46% helix, 17% strand | Q99YP9 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.75 | 0.81 | 56 | empty |
| 2 | 568 | 0.75 | 0.82 | 54 | empty |
| 3 | 626 | 0.75 | 0.81 | 52 | empty |
| 4 | 616 | 0.75 | 0.81 | 58 | empty |
| 5 | 601 | 0.74 | 0.81 | 57 | empty |
Interfaces
11 interfaces between chains.
- C–D · 758 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 731 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 215 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 191 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4B3K · Family 1 6-phospho-beta-D glycosidase from Streptococcus pyogenes · 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 Q99YP9
- Elsewhere: RCSB PDB 4B3K · PDBe 4B3K · UniProt Q99YP9
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