Research workbench
Enzyme-PHOSPHATE2 complex of pyridoxine 5'-phosphate synthase
Analyse Enzyme-PHOSPHATE2 complex of pyridoxine 5'-phosphate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IXQ
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine 5'-phosphate synthase
- UniProt
- P0A794
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyridoxine 5'-phosphate synthase | protein | 235 | 51% helix, 18% strand | P0A794 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.52 | 0.75 | 34 | empty |
| 2 | 138 | 0.50 | 0.79 | 25 | PO4 |
| 3 | 141 | 0.48 | 0.78 | 25 | PO4 |
| 4 | 131 | 0.46 | 0.78 | 33 | PO4 |
| 5 | 129 | 0.43 | 0.76 | 24 | PO4 |
Interfaces
2 interfaces between chains.
- B–D · 593 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 579 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1IXQ · Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P0A794 · AlphaFold monomer V2.0 prediction for pyridoxine 5'-phosphate synthase (P0A794) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A794
- Elsewhere: RCSB PDB 1IXQ · PDBe 1IXQ · UniProt P0A794
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