5ZWA
Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via Schiff base in protomer A and the product (PLP) in protomer B
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| 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 | 0016740 | molecular_function | transferase activity |
| A | 0042816 | biological_process | vitamin B6 metabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide 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 | 0016740 | molecular_function | transferase activity |
| 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 | 3 |
| Details | binding site for residue SO4 A 301 |
| Chain | Residue |
| A | GLU169 |
| A | HOH465 |
| B | GLU145 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 302 |
| Chain | Residue |
| A | GLN148 |
| A | HOH473 |
| B | GLN148 |
| B | ARG151 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 303 |
| Chain | Residue |
| A | HOH417 |
| A | HOH469 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 304 |
| Chain | Residue |
| A | HIS64 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 305 |
| Chain | Residue |
| A | GLU221 |
| A | LYS258 |
| B | EDO312 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 306 |
| Chain | Residue |
| A | LEU110 |
| A | TRP114 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 307 |
| Chain | Residue |
| A | ASP135 |
| A | ADP309 |
| A | HOH401 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 308 |
| Chain | Residue |
| A | SER34 |
| A | LEU279 |
| A | ILE280 |
| A | HOH464 |
| B | LYS45 |
| site_id | AC9 |
| Number of Residues | 21 |
| Details | binding site for residue ADP A 309 |
| Chain | Residue |
| A | ASN164 |
| A | THR200 |
| A | SER201 |
| A | THR209 |
| A | HIS225 |
| A | PRO226 |
| A | ARG227 |
| A | VAL228 |
| A | THR235 |
| A | GLY236 |
| A | ALA261 |
| A | VAL264 |
| A | MET268 |
| A | EDO307 |
| A | MG310 |
| A | MG311 |
| A | HOH403 |
| A | HOH410 |
| A | HOH419 |
| A | HOH424 |
| A | HOH436 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 310 |
| Chain | Residue |
| A | GLU167 |
| A | ADP309 |
| A | HOH410 |
| A | HOH419 |
| A | HOH424 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 311 |
| Chain | Residue |
| A | THR162 |
| A | ASN164 |
| A | THR200 |
| A | ADP309 |
| A | HOH410 |
| A | HOH426 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 312 |
| Chain | Residue |
| A | TYR101 |
| A | TYR141 |
| A | VAL142 |
| A | GLN143 |
| A | HOH406 |
| A | HOH416 |
| site_id | AD4 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 B 301 |
| Chain | Residue |
| B | THR136 |
| B | ASN164 |
| B | VAL165 |
| B | PHE166 |
| B | SER201 |
| B | HOH464 |
| B | HOH467 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue PLP B 302 |
| Chain | Residue |
| B | SER28 |
| B | PHE59 |
| B | PRO63 |
| B | TYR101 |
| B | TYR141 |
| B | HOH404 |
| B | HOH451 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue PO4 B 303 |
| Chain | Residue |
| B | LEU232 |
| B | LYS233 |
| B | GLY234 |
| B | THR235 |
| B | GOL313 |
| site_id | AD7 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 304 |
| Chain | Residue |
| B | EDO310 |
| B | HOH403 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 305 |
| Chain | Residue |
| B | GLN20 |
| B | THR21 |
| B | ARG50 |
| B | VAL51 |
| B | THR52 |
| B | HOH413 |
| site_id | AD9 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 306 |
| Chain | Residue |
| B | HOH403 |
| B | HOH498 |
| site_id | AE1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 307 |
| Chain | Residue |
| B | GLN249 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 309 |
| Chain | Residue |
| B | ASP22 |
| B | LYS95 |
| B | VAL248 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 310 |
| Chain | Residue |
| B | ALA79 |
| B | THR83 |
| B | EDO304 |
| B | HOH471 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 311 |
| Chain | Residue |
| B | GLN20 |
| B | ARG50 |
| A | CYS274 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 312 |
| Chain | Residue |
| A | EDO305 |
| A | HOH456 |
| B | VAL222 |
| B | HOH416 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 313 |
| Chain | Residue |
| B | ASP130 |
| B | THR162 |
| B | GLU167 |
| B | THR200 |
| B | PO4303 |
