MolNFT v1 · #50881 · protein
Pyridoxal phosphorylase B in complex with phosphite, glucose and inosine-5'-monophosphate
2SKE: “Pyridoxal phosphorylase B in complex with phosphite, glucose and inosine-5'-monophosphate”. X-ray diffraction, 4 ligands (PLP, IMP, GLC), 13 pockets (best druggability 0.84). MolNFT v1 #50881 on GenesisL1: 3D structure, binding…
- PDB
- 2SKE
- Type
- protein
- Length
- 830 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphorylase B
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, IMP, GLC, PO3
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal phosphorylase B (EC 2.4.1.1) | protein | 830 | 51% helix, 14% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- IMP · Inosinic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- PO3 · Phosphite ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.84 | 0.96 | 49 | GLC, PO3, PLP |
| 2 | 144 | 0.79 | 0.96 | 43 | empty |
| 3 | 294 | 0.70 | 0.84 | 34 | empty |
| 4 | 176 | 0.55 | 0.79 | 25 | empty |
| 5 | 206 | 0.51 | 0.77 | 22 | IMP |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2SKE · Pyridoxal phosphorylase B in complex with phosphite, glucose and inosine-5'-monophosphate · 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 P00489
- Elsewhere: RCSB PDB 2SKE · PDBe 2SKE · UniProt P00489
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