MolNFT v1 · #34369 · protein
Crystal structure of pyridoxal kinase from the escherichia COLI pdxk gene complexed with pyridoxal at 3.2 a resolution
2DDW · Pyridoxine kinase: “Crystal structure of pyridoxal kinase from the escherichia COLI pdxk gene complexed with pyridoxal at 3.2 a…”. X-ray diffraction, 1 ligand (PXL), 5 pockets (best druggability 0.78). MolNFT v1 #34369 on GenesisL1…
- PDB
- 2DDW
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine kinase
- EC
- 2.7.1.35
- UniProt
- P40191
- Ligands
- PXL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxine kinase (EC 2.7.1.35) | protein | 263 | 35% helix, 14% strand | P40191 |
| B | Pyridoxine kinase (EC 2.7.1.35) | protein | 261 | 38% helix, 15% strand | P40191 |
Ligands and binding sites
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.78 | 0.80 | 54 | empty |
| 2 | 518 | 0.73 | 0.82 | 46 | PXL |
| 3 | 516 | 0.68 | 0.78 | 57 | PXL |
| 4 | 77 | 0.46 | 0.82 | 19 | empty |
| 5 | 56 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1644 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2DDW · Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- P40191 · AlphaFold monomer V2.0 prediction for PYRIDOXINE/PYRIDOXAL/PYRIDOXAMINE kinase (P40191) · 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 P40191
- Elsewhere: RCSB PDB 2DDW · PDBe 2DDW · UniProt P40191
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