MolNFT v1 · #142192 · protein
Crystal structure of pyridoxal kinase (pdxk) from salmonella typhimurium
5ZW9 · Pyridoxalkinase: “Crystal structure of pyridoxal kinase (pdxk) from salmonella typhimurium”. X-ray diffraction, 2 ligands (MG, PO4), 3 pockets (best druggability 0.79). MolNFT v1 #142192 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZW9
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxalkinase
- EC
- 2.7.1.35
- UniProt
- A0A0M0PWM4
- Ligands
- MG, PO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxalkinase (EC 2.7.1.35) | protein | 266 | 40% helix, 20% strand | A0A0M0PWM4 |
| B | Pyridoxalkinase (EC 2.7.1.35) | protein | 260 | 40% helix, 19% strand | A0A0M0PWM4 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.79 | 0.83 | 67 | empty |
| 2 | 476 | 0.75 | 0.83 | 48 | PO4, MG |
| 3 | 427 | 0.66 | 0.79 | 43 | EDO |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5ZW9 · Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0M0PWM4
- Elsewhere: RCSB PDB 5ZW9 · PDBe 5ZW9 · UniProt A0A0M0PWM4
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