Research workbench
Crystal structure of bifidobacterium adolescentis GH3 beta-glucosidase
Analyse Crystal structure of bifidobacterium adolescentis GH3 beta-glucosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WAB
- Type
- protein
- Length
- 2,688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative beta-glucosidase
- UniProt
- A1A2P2
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative beta-glucosidase | protein | 674 | 31% helix, 23% strand | A1A2P2 |
| B | Putative beta-glucosidase | protein | 659 | 31% helix, 24% strand | A1A2P2 |
| C | Putative beta-glucosidase | protein | 654 | 31% helix, 24% strand | A1A2P2 |
| D | Putative beta-glucosidase | protein | 701 | 34% helix, 22% strand | A1A2P2 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.75 | 0.78 | 118 | empty |
| 2 | 980 | 0.75 | 0.78 | 116 | empty |
| 3 | 53 | 0.72 | 0.99 | 22 | empty |
| 4 | 52 | 0.70 | 0.98 | 21 | empty |
| 5 | 125 | 0.65 | 0.88 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1278 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1157 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WAB · Crystal Structure of Bifidobacterium adolescentis GH3 beta-glucosidase · 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 A1A2P2
- Elsewhere: RCSB PDB 5WAB · PDBe 5WAB · UniProt A1A2P2
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