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Pyridoxal phosphate biosynthetic protein pdxj from campylobacter jejuni

Analyse Pyridoxal phosphate biosynthetic protein pdxj from campylobacter jejuni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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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