Research workbench
Enzyme-substrate complex of pyridoxine 5'-phosphate synthase
Analyse Enzyme-substrate 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
- 1IXN
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine 5'-phosphate synthase
- UniProt
- P0A794
- Ligands
- DXP, G3P
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyridoxine 5'-phosphate synthase | protein | 242 | 47% helix, 17% strand | P0A794 |
Ligands and binding sites
- DXP · 1-deoxy-D-xylulose-5-phosphate · ligand · 4 copies · chains A, B, C, D
- G3P · Sn-glycerol-3-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.68 | 0.89 | 26 | DXP, G3P |
| 2 | 172 | 0.66 | 0.86 | 30 | DXP, G3P |
| 3 | 138 | 0.65 | 0.88 | 25 | DXP, G3P |
| 4 | 152 | 0.63 | 0.85 | 28 | DXP, G3P |
| 5 | 183 | 0.46 | 0.75 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–D · 586 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1IXN · Enzyme-Substrate 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 0.97
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 1IXN · PDBe 1IXN · UniProt P0A794
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