MolNFT v1 · #14330 · protein
1.96 a crystal structure of pyridoxine 5'-phosphate synthase in complex with 1-deoxy-D-xylulose phosphate
1M5W · Pyridoxal phosphate biosynthetic protein pdxj: “1.96 a crystal structure of pyridoxine 5'-phosphate synthase in complex with 1-deoxy-D-xylulose phosphate”. X-ray diffraction, 2 ligands (DXP, PO4), 19 pockets (best druggability…
- PDB
- 1M5W
- Type
- protein
- Length
- 1,936 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate biosynthetic protein pdxj
- UniProt
- P0A794
- Ligands
- DXP, PO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Pyridoxal phosphate biosynthetic protein pdxj | protein | 242 | 49% helix, 17% strand | P0A794 |
Ligands and binding sites
- DXP · 1-deoxy-D-xylulose-5-phosphate · ligand · 6 copies · chains A, E, B, C, F, G
- PO4 · Phosphate ion · ion · 2 copies · chains A, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.81 | 0.83 | 154 | empty |
| 2 | 1057 | 0.81 | 0.83 | 131 | empty |
| 3 | 281 | 0.77 | 0.89 | 63 | DXP, PO4 |
| 4 | 392 | 0.76 | 0.86 | 59 | empty |
| 5 | 451 | 0.74 | 0.84 | 63 | DXP, PO4 |
Interfaces
16 interfaces between chains.
- A–E · 1173 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 1158 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 1104 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 1101 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 578 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1M5W · 1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with… · the same entry in another collection · chain F against F, 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 1M5W · PDBe 1M5W · UniProt P0A794
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