MolNFT v1 · #20240 · protein
Pdxa protein; NAD-dependent DEHYDROGENASE/CARBOXYLASE; subunit of pyridoxine phosphate biosynthetic protein pdxj- pdxa [salmonella typhimurium]
1R8K · 4-hydroxythreonine-4-phosphate dehydrogenase 1: “Pdxa protein; NAD-dependent DEHYDROGENASE/CARBOXYLASE; subunit of pyridoxine phosphate biosynthetic protein…”. X-ray diffraction, 3 ligands (CO, SO4, CL), 5 pockets (best druggability…
- PDB
- 1R8K
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxythreonine-4-phosphate dehydrogenase 1
- EC
- 1.1.1.262
- UniProt
- P58717
- Ligands
- CO, SO4, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxythreonine-4-phosphate dehydrogenase 1 (EC 1.1.1.262) | protein | 327 | 40% helix, 18% strand | P58717 |
| B | 4-hydroxythreonine-4-phosphate dehydrogenase 1 (EC 1.1.1.262) | protein | 326 | 39% helix, 18% strand | P58717 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.71 | 0.82 | 51 | CO, SO4 |
| 2 | 465 | 0.70 | 0.81 | 51 | SO4 |
| 3 | 78 | 0.37 | 0.77 | 21 | empty |
| 4 | 55 | 0.35 | 0.78 | 14 | empty |
| 5 | 80 | 0.34 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1765 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1R8K · Pdxa protein; NAD-dependent DEHYDROGENASE/CARBOXYLASE; subunit of pyridoxine phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P58717 · AlphaFold monomer V2.0 prediction for 4-hydroxythreonine-4-phosphate dehydrogenase… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P58717
- Elsewhere: RCSB PDB 1R8K · PDBe 1R8K · UniProt P58717
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