Research workbench
Structure of the pyridoxal kinase from staphylococcus aureus in complex with AMP-pcp and 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
- 4C5N
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine kinase
- EC
- 2.7.1.35
- UniProt
- C8MK44
- Ligands
- ACP, PXL, UEG, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 268 | 41% helix, 22% strand | C8MK44 |
| B | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 269 | 41% helix, 22% strand | C8MK44 |
| C | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 266 | 42% helix, 23% strand | C8MK44 |
| D | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 269 | 41% helix, 22% strand | C8MK44 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 3 copies · chains A, B, C
- UEG · 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol · ligand · chains D
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.81 | 0.82 | 123 | PXL, ACP |
| 2 | 412 | 0.75 | 0.85 | 51 | UEG, ACP |
| 3 | 385 | 0.69 | 0.81 | 45 | PXL, ACP |
| 4 | 431 | 0.67 | 0.79 | 46 | PXL, ACP |
| 5 | 250 | 0.56 | 0.78 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1960 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1952 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 320 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 107 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4C5N · Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP and… · 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 C8MK44
- Elsewhere: RCSB PDB 4C5N · PDBe 4C5N · UniProt C8MK44
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