5ZWB
Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via a Schiff base
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005829 | cellular_component | cytosol |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0008478 | molecular_function | pyridoxal kinase activity |
| A | 0008902 | molecular_function | hydroxymethylpyrimidine kinase activity |
| A | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016310 | biological_process | phosphorylation |
| A | 0042816 | biological_process | vitamin B6 metabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005829 | cellular_component | cytosol |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0008478 | molecular_function | pyridoxal kinase activity |
| B | 0008902 | molecular_function | hydroxymethylpyrimidine kinase activity |
| B | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016310 | biological_process | phosphorylation |
| B | 0042816 | biological_process | vitamin B6 metabolic process |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 301 |
| Chain | Residue |
| A | ADP304 |
| A | HOH404 |
| A | HOH406 |
| A | HOH421 |
| A | HOH431 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 302 |
| Chain | Residue |
| B | ARG177 |
| A | GLN143 |
| A | GLU145 |
| A | HOH515 |
| B | GLU169 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 303 |
| Chain | Residue |
| A | ASP14 |
| A | EDO306 |
| site_id | AC4 |
| Number of Residues | 20 |
| Details | binding site for residue ADP A 304 |
| Chain | Residue |
| A | ASN164 |
| A | THR200 |
| A | SER201 |
| A | VAL212 |
| A | HIS225 |
| A | PRO226 |
| A | ARG227 |
| A | VAL228 |
| A | THR235 |
| A | GLY236 |
| A | ALA261 |
| A | VAL264 |
| A | MET268 |
| A | MG301 |
| A | EDO311 |
| A | MG312 |
| A | HOH406 |
| A | HOH413 |
| A | HOH431 |
| A | HOH486 |
| site_id | AC5 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 305 |
| Chain | Residue |
| A | HOH454 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 306 |
| Chain | Residue |
| A | ASN86 |
| A | SO4303 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 307 |
| Chain | Residue |
| A | HIS64 |
| A | TYR65 |
| A | ASP277 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 308 |
| Chain | Residue |
| A | ASN37 |
| A | SER38 |
| A | ALA53 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 309 |
| Chain | Residue |
| A | TYR65 |
| A | LYS66 |
| A | HOH405 |
| A | HOH419 |
| B | GLU87 |
| B | ARG88 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 310 |
| Chain | Residue |
| A | LEU279 |
| A | ILE280 |
| A | LEU281 |
| A | HOH403 |
| A | HOH407 |
| B | LEU19 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 311 |
| Chain | Residue |
| A | ASP137 |
| A | ADP304 |
| A | HOH409 |
| A | HOH414 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 312 |
| Chain | Residue |
| A | THR162 |
| A | PRO163 |
| A | ASN164 |
| A | THR200 |
| A | ADP304 |
| A | HOH406 |
| A | HOH475 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue TRS B 301 |
| Chain | Residue |
| B | ASP130 |
| B | TYR141 |
| B | THR162 |
| B | ASN164 |
| B | GLU167 |
| B | THR200 |
| B | GLY236 |
| B | EDO305 |
| B | HOH451 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 302 |
| Chain | Residue |
| A | HOH436 |
| B | GLN143 |
| B | HOH417 |
| B | HOH446 |
| B | HOH447 |
| B | HOH558 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 303 |
| Chain | Residue |
| A | GLN148 |
| A | HOH499 |
| B | GLN148 |
| B | ARG151 |
| B | THR152 |
| B | ASP192 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 304 |
| Chain | Residue |
| A | CYS276 |
| B | GLN20 |
| B | ARG50 |
| B | HOH428 |
| site_id | AD8 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 305 |
| Chain | Residue |
| B | GLN27 |
| B | THR99 |
| B | GLY100 |
| B | ASP130 |
| B | ASP237 |
| B | CYS240 |
| B | TRS301 |
| B | EDO308 |
| B | HOH418 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 306 |
| Chain | Residue |
| B | TYR101 |
| B | ASP237 |
| B | HOH451 |
| B | HOH508 |
| B | SER28 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 307 |
| Chain | Residue |
| B | THR152 |
| B | HIS153 |
| site_id | AE2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 308 |
| Chain | Residue |
| B | GLN27 |
| B | ALA40 |
| B | THR98 |
| B | ASP237 |
| B | CYS240 |
| B | ALA241 |
| B | VAL244 |
| B | EDO305 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 309 |
| Chain | Residue |
| B | PRO123 |
| B | GLU124 |
| B | CME126 |
| B | GLN159 |
