Research workbench
Structure of the pyridoxal kinase from staphylococcus aureus in complex with pyridoxal
Analyse Structure of the pyridoxal kinase from staphylococcus aureus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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