MolNFT v1 · #114057 · protein
Beta-1,2-mannobiose phosphorylase from listeria innocua - glycerol complex
5B0P · LIN0857 protein: “Beta-1,2-mannobiose phosphorylase from listeria innocua - glycerol complex”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.76). MolNFT v1 #114057 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B0P
- 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
- SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% 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 | 5% helix, 50% strand | Q92DF6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.76 | 0.82 | 64 | SO4, GOL |
| 2 | 437 | 0.75 | 0.84 | 54 | SO4, GOL |
| 3 | 172 | 0.54 | 0.79 | 23 | empty |
| 4 | 146 | 0.50 | 0.78 | 20 | empty |
| 5 | 66 | 0.33 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1735 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5B0P · Beta-1,2-Mannobiose phosphorylase from Listeria innocua - glycerol 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 5B0P · PDBe 5B0P · UniProt Q92DF6
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