MolNFT v1 · #73584 · protein
Pyridoxal phosphate biosynthetic protein pdxj from campylobacter jejuni
3O6C · Pyridoxine 5'-phosphate synthase: “Pyridoxal phosphate biosynthetic protein pdxj from campylobacter jejuni”. X-ray diffraction, 1 ligand (PO4), 1 pocket (best druggability 0.58). MolNFT v1 #73584 on GenesisL1: 3D structure, binding…
- PDB
- 3O6C
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine 5'-phosphate synthase
- EC
- 2.6.99.2
- UniProt
- Q9PN59
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 259 | 50% helix, 15% strand | Q9PN59 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.58 | 0.79 | 29 | PO4 |
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3O6C · Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PN59 · AlphaFold monomer V2.0 prediction for pyridoxine 5'-phosphate synthase (Q9PN59) · 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 Q9PN59
- Elsewhere: RCSB PDB 3O6C · PDBe 3O6C · UniProt Q9PN59
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