Research workbench
Beta-1,2-mannobiose phosphorylase from listeria innocua - beta-1,2- mannotriose complex
Analyse Beta-1,2-mannobiose phosphorylase from listeria innocua - beta-1,2- mannotriose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B0S
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIN0857 protein
- UniProt
- Q92DF6
- Ligands
- BMA, MAN, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN0857 protein | protein | 354 | 5% helix, 51% strand | Q92DF6 |
| B | LIN0857 protein | protein | 355 | 6% helix, 50% strand | Q92DF6 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.77 | 0.84 | 56 | MAN, BMA, SO4 |
| 2 | 514 | 0.76 | 0.84 | 57 | MAN, BMA, SO4 |
| 3 | 167 | 0.52 | 0.78 | 21 | empty |
| 4 | 143 | 0.51 | 0.79 | 19 | empty |
| 5 | 61 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1737 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5B0S · Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannotriose complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q92DF6 · AlphaFold monomer V2.0 prediction for beta-1,2-mannobiose phosphorylase (Q92DF6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q92DF6
- Elsewhere: RCSB PDB 5B0S · PDBe 5B0S · UniProt Q92DF6
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