MolNFT v1 · #87583 · protein
Structure of the pyridoxal kinase from staphylococcus aureus in complex with pyridoxal
4C5L · Phosphomethylpyrimidine kinase: “Structure of the pyridoxal kinase from staphylococcus aureus in complex with pyridoxal”. X-ray diffraction, 3 ligands (UEG, PXL, SO4), 10 pockets (best druggability 0.86). MolNFT v1 #87583 on…
- PDB
- 4C5L
- Type
- protein
- Length
- 1,073 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine kinase
- EC
- 2.7.1.35
- UniProt
- Q99W31
- Ligands
- UEG, PXL, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 264 | 41% helix, 22% strand | Q99W31 |
| B | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 271 | 39% helix, 22% strand | Q99W31 |
| C, D | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 269 | 42% helix, 23% strand | Q99W31 |
Ligands and binding sites
- UEG · 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol · ligand · 3 copies · chains A, C, D
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.86 | 0.89 | 83 | empty |
| 2 | 396 | 0.75 | 0.85 | 49 | UEG, SO4 |
| 3 | 359 | 0.72 | 0.84 | 48 | UEG |
| 4 | 296 | 0.68 | 0.83 | 44 | UEG, SO4 |
| 5 | 68 | 0.55 | 0.88 | 19 | PXL, SO4 |
Interfaces
5 interfaces between chains.
- B–C · 1931 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1902 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 479 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 278 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 121 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4C5L · Structure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal · 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 Q99W31
- Elsewhere: RCSB PDB 4C5L · PDBe 4C5L · UniProt Q99W31
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.