MolNFT v1 · #34363 · protein
Crystal structure of pyridoxal kinase from the escherichia COLI pdxk gene at 2.6 a resolution
2DDO · Pyridoxine kinase: “Crystal structure of pyridoxal kinase from the escherichia COLI pdxk gene at 2.6 a resolution”. X-ray diffraction, 3 ligands (ATP, MG, PO4), 4 pockets (best druggability 0.77). MolNFT v1 #34363 on GenesisL1: 3D…
- PDB
- 2DDO
- Type
- protein
- Length
- 531 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
- ATP, MG, PO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxine kinase (EC 2.7.1.35) | protein | 263 | 40% helix, 21% strand | P40191 |
| B | Pyridoxine kinase (EC 2.7.1.35) | protein | 268 | 38% helix, 21% strand | P40191 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.77 | 0.81 | 52 | empty |
| 2 | 619 | 0.75 | 0.81 | 48 | MG, ATP |
| 3 | 498 | 0.66 | 0.78 | 43 | PO4 |
| 4 | 54 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1652 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2DDO · Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK gene at 2.6 A… · the same entry in another collection · chain A against A, 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 0.99
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 P40191
- Elsewhere: RCSB PDB 2DDO · PDBe 2DDO · UniProt P40191
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