6YK0
Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma-S
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0008478 | molecular_function | pyridoxal kinase activity |
| A | 0008614 | biological_process | pyridoxine metabolic process |
| A | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0030955 | molecular_function | potassium ion binding |
| A | 0031402 | molecular_function | sodium ion binding |
| A | 0031403 | molecular_function | lithium ion binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0042817 | biological_process | pyridoxal metabolic process |
| A | 0042818 | biological_process | pyridoxamine metabolic process |
| A | 0042822 | biological_process | pyridoxal phosphate metabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0008478 | molecular_function | pyridoxal kinase activity |
| B | 0008614 | biological_process | pyridoxine metabolic process |
| B | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0030955 | molecular_function | potassium ion binding |
| B | 0031402 | molecular_function | sodium ion binding |
| B | 0031403 | molecular_function | lithium ion binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0042817 | biological_process | pyridoxal metabolic process |
| B | 0042818 | biological_process | pyridoxamine metabolic process |
| B | 0042822 | biological_process | pyridoxal phosphate metabolic process |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0008270 | molecular_function | zinc ion binding |
| C | 0008478 | molecular_function | pyridoxal kinase activity |
| C | 0008614 | biological_process | pyridoxine metabolic process |
| C | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| C | 0016301 | molecular_function | kinase activity |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
| C | 0030170 | molecular_function | pyridoxal phosphate binding |
| C | 0030955 | molecular_function | potassium ion binding |
| C | 0031402 | molecular_function | sodium ion binding |
| C | 0031403 | molecular_function | lithium ion binding |
| C | 0042803 | molecular_function | protein homodimerization activity |
| C | 0042817 | biological_process | pyridoxal metabolic process |
| C | 0042818 | biological_process | pyridoxamine metabolic process |
| C | 0042822 | biological_process | pyridoxal phosphate metabolic process |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0008478 | molecular_function | pyridoxal kinase activity |
| D | 0008614 | biological_process | pyridoxine metabolic process |
| D | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| D | 0016301 | molecular_function | kinase activity |
| D | 0016740 | molecular_function | transferase activity |
| D | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
| D | 0030170 | molecular_function | pyridoxal phosphate binding |
| D | 0030955 | molecular_function | potassium ion binding |
| D | 0031402 | molecular_function | sodium ion binding |
| D | 0031403 | molecular_function | lithium ion binding |
| D | 0042803 | molecular_function | protein homodimerization activity |
| D | 0042817 | biological_process | pyridoxal metabolic process |
| D | 0042818 | biological_process | pyridoxamine metabolic process |
| D | 0042822 | biological_process | pyridoxal phosphate metabolic process |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue PG4 A 401 |
| Chain | Residue |
| A | PHE43 |
| A | THR47 |
| A | TYR84 |
| B | ARG224 |
| site_id | AC2 |
| Number of Residues | 15 |
| Details | binding site for residue AGS A 402 |
| Chain | Residue |
| A | SER187 |
| A | MET223 |
| A | ARG224 |
| A | LYS225 |
| A | VAL226 |
| A | ALA228 |
| A | THR233 |
| A | GLY234 |
| A | MET263 |
| A | LEU267 |
| A | ASP113 |
| A | ASP118 |
| A | ASN150 |
| A | GLU153 |
| A | THR186 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 403 |
| Chain | Residue |
| A | GLU4 |
| A | CYS5 |
| A | LEU31 |
| A | GLY32 |
| A | LYS247 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | binding site for residue PG4 A 404 |
| Chain | Residue |
| A | ARG6 |
| A | ASP78 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 405 |
| Chain | Residue |
| A | HIS63 |
| A | TYR66 |
| A | GLU67 |
| A | MET93 |
| A | ASP96 |
| A | GLU100 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | GLY159 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | ASN39 |
| A | GLN42 |
| B | ASN39 |
| B | GLN42 |
| site_id | AC8 |
| Number of Residues | 16 |
| Details | binding site for residue AGS B 401 |
| Chain | Residue |
| B | ASP113 |
| B | VAL115 |
| B | ASP118 |
| B | ASN150 |
| B | GLU153 |
| B | THR186 |
| B | SER187 |
| B | MET223 |
| B | ARG224 |
| B | VAL226 |
| B | ALA228 |
| B | THR233 |
| B | GLY234 |
| B | MET263 |
| B | LEU267 |
| B | EDO409 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 402 |
| Chain | Residue |
| B | ARG272 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 403 |
| Chain | Residue |
| B | CYS5 |
| B | LEU31 |
| B | GLY32 |
| B | PHE33 |
| B | HIS246 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 404 |
| Chain | Residue |
| B | HIS46 |
| B | THR47 |
| site_id | AD3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| B | GLU155 |
| B | LEU156 |
| B | GLY159 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | SER106 |
| B | LEU108 |
| B | ASP145 |
| site_id | AD5 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | ASP302 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| B | SER40 |
| B | VAL56 |
| B | LEU57 |
| B | THR85 |
| B | PHE90 |
| site_id | AD7 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 409 |
| Chain | Residue |
| B | LEU199 |
| B | AGS401 |
| site_id | AD8 |
| Number of Residues | 14 |
| Details | binding site for residue AGS C 401 |
| Chain | Residue |
| C | ASP113 |
| C | GLY117 |
| C | ASP118 |
| C | ASN150 |
| C | GLU153 |
| C | THR186 |
| C | SER187 |
| C | MET223 |
| C | ARG224 |
| C | VAL226 |
| C | ALA228 |
| C | THR233 |
| C | GLY234 |
| C | LEU267 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 402 |
| Chain | Residue |
| C | LYS102 |
| C | PRO142 |
| C | ASP145 |
| C | GLY179 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue GOL C 403 |
| Chain | Residue |
| C | HIS63 |
| C | GLU67 |
| C | MET93 |
| C | ILE97 |
| C | GLU100 |
| site_id | AE2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 404 |
| Chain | Residue |
| C | THR47 |
| C | PHE43 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 405 |
| Chain | Residue |
| C | LEU31 |
| C | GLY32 |
| C | EDO406 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 406 |
| Chain | Residue |
| C | LEU31 |
| C | PHE33 |
| C | ALA243 |
| C | EDO405 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 407 |
| Chain | Residue |
| C | ARG86 |
| C | TYR127 |
| C | VAL128 |
| C | PRO129 |
| C | GLN130 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 408 |
| Chain | Residue |
| C | ASN39 |
| C | GLN42 |
| D | ASN39 |
| D | GLN42 |
| site_id | AE7 |
| Number of Residues | 14 |
| Details | binding site for residue AGS D 401 |
| Chain | Residue |
| D | VAL115 |
| D | ASP118 |
| D | ASN150 |
| D | GLU153 |
| D | THR186 |
| D | SER187 |
| D | MET223 |
| D | ARG224 |
| D | VAL226 |
| D | ALA228 |
| D | THR233 |
| D | GLY234 |
| D | PHE237 |
| D | LEU267 |
| site_id | AE8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 402 |
| Chain | Residue |
| D | HIS46 |
| D | THR47 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"O00764","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 56 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"O00764","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"O00764","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
