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 | 0000287 | molecular_function | magnesium ion binding |
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 | 0042816 | biological_process | vitamin B6 metabolic process |
A | 0046872 | molecular_function | metal ion binding |
B | 0000287 | molecular_function | magnesium ion binding |
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 | 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 |