1RFU
Crystal structure of pyridoxal kinase complexed with ADP and PLP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008478 | molecular_function | pyridoxal 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 | 0005524 | molecular_function | ATP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008478 | molecular_function | pyridoxal 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 |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0008478 | molecular_function | pyridoxal kinase activity |
| C | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| C | 0016301 | molecular_function | kinase activity |
| C | 0042816 | biological_process | vitamin B6 metabolic process |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0008478 | molecular_function | pyridoxal kinase activity |
| D | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| D | 0016301 | molecular_function | kinase activity |
| D | 0042816 | biological_process | vitamin B6 metabolic process |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0005829 | cellular_component | cytosol |
| E | 0008478 | molecular_function | pyridoxal kinase activity |
| E | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| E | 0016301 | molecular_function | kinase activity |
| E | 0042816 | biological_process | vitamin B6 metabolic process |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0005524 | molecular_function | ATP binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0005829 | cellular_component | cytosol |
| F | 0008478 | molecular_function | pyridoxal kinase activity |
| F | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| F | 0016301 | molecular_function | kinase activity |
| F | 0042816 | biological_process | vitamin B6 metabolic process |
| F | 0046872 | molecular_function | metal ion binding |
| G | 0005524 | molecular_function | ATP binding |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0005829 | cellular_component | cytosol |
| G | 0008478 | molecular_function | pyridoxal kinase activity |
| G | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| G | 0016301 | molecular_function | kinase activity |
| G | 0042816 | biological_process | vitamin B6 metabolic process |
| G | 0046872 | molecular_function | metal ion binding |
| H | 0005524 | molecular_function | ATP binding |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0005829 | cellular_component | cytosol |
| H | 0008478 | molecular_function | pyridoxal kinase activity |
| H | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| H | 0016301 | molecular_function | kinase activity |
| H | 0042816 | biological_process | vitamin B6 metabolic process |
| H | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN A 403 |
| Chain | Residue |
| A | TYR127 |
| A | PLP401 |
| A | ADP402 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN B 1403 |
| Chain | Residue |
| B | VAL115 |
| B | PLP1401 |
| B | ADP1402 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN C 2403 |
| Chain | Residue |
| C | VAL115 |
| C | PLP2401 |
| C | ADP2402 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 3403 |
| Chain | Residue |
| D | ASP113 |
| D | VAL115 |
| D | PLP3401 |
| D | ADP3402 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN E 4403 |
| Chain | Residue |
| E | ASP113 |
| E | VAL115 |
| E | PLP4401 |
| E | ADP4402 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN F 5403 |
| Chain | Residue |
| F | ASP113 |
| F | VAL115 |
| F | PLP5401 |
| F | ADP5402 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN G 6403 |
| Chain | Residue |
| G | ASP113 |
| G | PLP6401 |
| G | ADP6402 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN H 7403 |
| Chain | Residue |
| H | ASP113 |
| H | VAL115 |
| H | PLP7401 |
| H | ADP7402 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP A 401 |
| Chain | Residue |
| A | SER12 |
| A | VAL19 |
| A | THR47 |
| A | TYR84 |
| A | TYR127 |
| A | VAL231 |
| A | GLY232 |
| A | THR233 |
| A | GLY234 |
| A | ASP235 |
| A | ADP402 |
| A | ZN403 |
| site_id | BC1 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE ADP A 402 |
| Chain | Residue |
| A | ASN150 |
| A | THR186 |
| A | SER187 |
| A | LEU199 |
| A | MET223 |
| A | HIS224 |
| A | LYS225 |
| A | VAL226 |
| A | ALA228 |
| A | THR233 |
| A | GLY234 |
| A | PHE237 |
| A | MET263 |
| A | LEU267 |
| A | PLP401 |
| A | ZN403 |
| site_id | BC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP B 1401 |
| Chain | Residue |
| B | SER12 |
| B | VAL19 |
| B | THR47 |
| B | TYR84 |
| B | TYR127 |
| B | VAL231 |
| B | GLY232 |
| B | THR233 |
| B | GLY234 |
| B | ASP235 |
| B | ADP1402 |
| B | ZN1403 |
| site_id | BC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE ADP B 1402 |
| Chain | Residue |
| B | THR186 |
| B | SER187 |
| B | MET223 |
| B | HIS224 |
| B | LYS225 |
| B | VAL226 |
| B | ALA228 |
| B | THR233 |
| B | GLY234 |
| B | MET263 |
| B | LEU267 |
| B | PLP1401 |
| B | ZN1403 |
| site_id | BC4 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP C 2401 |
| Chain | Residue |
| C | SER12 |
| C | VAL19 |
| C | THR47 |
| C | TYR84 |
| C | TYR127 |
| C | VAL231 |
| C | GLY232 |
| C | THR233 |
| C | GLY234 |
| C | ASP235 |
| C | ADP2402 |
| C | ZN2403 |
| site_id | BC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE ADP C 2402 |
| Chain | Residue |
| C | LYS225 |
| C | VAL226 |
| C | ALA228 |
| C | THR233 |
| C | GLY234 |
| C | MET263 |
| C | LEU267 |
| C | PLP2401 |
| C | ZN2403 |
| C | ASN150 |
| C | THR186 |
| C | SER187 |
| C | LEU199 |
| C | MET223 |
| C | HIS224 |
| site_id | BC6 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP D 3401 |
| Chain | Residue |
| D | SER12 |
| D | VAL19 |
| D | THR47 |
| D | TYR84 |
| D | TYR127 |
| D | VAL231 |
| D | GLY232 |
| D | THR233 |
| D | GLY234 |
| D | ASP235 |
| D | ADP3402 |
| D | ZN3403 |
| site_id | BC7 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE ADP D 3402 |
| Chain | Residue |
| D | ASN150 |
| D | THR186 |
| D | SER187 |
| D | LEU199 |
| D | MET223 |
| D | HIS224 |
| D | LYS225 |
| D | VAL226 |
| D | ALA228 |
| D | THR233 |
| D | GLY234 |
| D | MET263 |
| D | LEU267 |
| D | PLP3401 |
| D | ZN3403 |
| site_id | BC8 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP E 4401 |
| Chain | Residue |
| E | SER12 |
| E | VAL19 |
| E | THR47 |
| E | TYR84 |
| E | TYR127 |
| E | VAL231 |
| E | GLY232 |
| E | THR233 |
| E | GLY234 |
| E | ASP235 |
| E | ADP4402 |
| E | ZN4403 |
| site_id | BC9 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE ADP E 4402 |
| Chain | Residue |
| E | ASN150 |
| E | THR186 |
| E | SER187 |
| E | MET223 |
| E | HIS224 |
| E | LYS225 |
| E | VAL226 |
| E | ALA228 |
| E | THR233 |
| E | GLY234 |
| E | MET263 |
| E | LEU267 |
| E | PLP4401 |
| E | ZN4403 |
| site_id | CC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE PLP F 5401 |
| Chain | Residue |
| F | SER12 |
| F | VAL19 |
| F | THR47 |
| F | TYR84 |
| F | TYR127 |
| F | VAL231 |
| F | GLY232 |
| F | GLY234 |
| F | ASP235 |
| F | ADP5402 |
| F | ZN5403 |
| site_id | CC2 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE ADP F 5402 |
| Chain | Residue |
| F | ASN150 |
| F | THR186 |
| F | SER187 |
| F | MET223 |
| F | HIS224 |
| F | LYS225 |
| F | VAL226 |
| F | ALA228 |
| F | THR233 |
| F | GLY234 |
| F | MET263 |
| F | LEU267 |
| F | PLP5401 |
| F | ZN5403 |
| site_id | CC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE PLP G 6401 |
| Chain | Residue |
| G | SER12 |
| G | VAL19 |
| G | THR47 |
| G | TYR84 |
| G | TYR127 |
| G | VAL231 |
| G | GLY232 |
| G | GLY234 |
| G | ASP235 |
| G | ADP6402 |
| G | ZN6403 |
| site_id | CC4 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE ADP G 6402 |
| Chain | Residue |
| G | ASN150 |
| G | THR186 |
| G | SER187 |
| G | MET223 |
| G | HIS224 |
| G | LYS225 |
| G | VAL226 |
| G | ALA228 |
| G | THR233 |
| G | GLY234 |
| G | MET263 |
| G | LEU267 |
| G | PLP6401 |
| G | ZN6403 |
| site_id | CC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP H 7401 |
| Chain | Residue |
| H | SER12 |
| H | VAL19 |
| H | THR47 |
| H | TYR84 |
| H | TYR127 |
| H | VAL231 |
| H | GLY232 |
| H | THR233 |
| H | GLY234 |
| H | ASP235 |
| H | ADP7402 |
| H | ZN7403 |
| site_id | CC6 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE ADP H 7402 |
| Chain | Residue |
| H | ASN150 |
| H | THR186 |
| H | SER187 |
| H | MET223 |
| H | HIS224 |
| H | LYS225 |
| H | VAL226 |
| H | ALA228 |
| H | THR233 |
| H | GLY234 |
| H | MET263 |
| H | LEU267 |
| H | PLP7401 |
| H | ZN7403 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:O00764 |
| Chain | Residue | Details |
| A | ASP235 | |
| B | ASP235 | |
| C | ASP235 | |
| D | ASP235 | |
| E | ASP235 | |
| F | ASP235 | |
| G | ASP235 | |
| H | ASP235 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14722069, ECO:0007744|PDB:1RFT |
| Chain | Residue | Details |
| A | SER12 | |
| D | SER12 | |
| D | THR47 | |
| D | ASP235 | |
| E | SER12 | |
| E | THR47 | |
| E | ASP235 | |
| F | SER12 | |
| F | THR47 | |
| F | ASP235 | |
| G | SER12 | |
| A | THR47 | |
| G | THR47 | |
| G | ASP235 | |
| H | SER12 | |
| H | THR47 | |
| H | ASP235 | |
| A | ASP235 | |
| B | SER12 | |
| B | THR47 | |
| B | ASP235 | |
| C | SER12 | |
| C | THR47 | |
| C | ASP235 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12235162, ECO:0000269|PubMed:14722069, ECO:0007744|PDB:1LHR, ECO:0007744|PDB:1RFT |
| Chain | Residue | Details |
| A | ASP113 | |
| D | ASP113 | |
| D | THR148 | |
| D | THR186 | |
| E | ASP113 | |
| E | THR148 | |
| E | THR186 | |
| F | ASP113 | |
| F | THR148 | |
| F | THR186 | |
| G | ASP113 | |
| A | THR148 | |
| G | THR148 | |
| G | THR186 | |
| H | ASP113 | |
| H | THR148 | |
| H | THR186 | |
| A | THR186 | |
| B | ASP113 | |
| B | THR148 | |
| B | THR186 | |
| C | ASP113 | |
| C | THR148 | |
| C | THR186 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14722069, ECO:0007744|PDB:1RFU |
| Chain | Residue | Details |
| A | TYR127 | |
| E | GLY232 | |
| F | TYR127 | |
| F | GLY232 | |
| G | TYR127 | |
| G | GLY232 | |
| H | TYR127 | |
| H | GLY232 | |
| A | GLY232 | |
| B | TYR127 | |
| B | GLY232 | |
| C | TYR127 | |
| C | GLY232 | |
| D | TYR127 | |
| D | GLY232 | |
| E | TYR127 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12235162, ECO:0000269|PubMed:14722069, ECO:0007744|PDB:1LHR |
| Chain | Residue | Details |
| A | ASN150 | |
| B | ASN150 | |
| C | ASN150 | |
| D | ASN150 | |
| E | ASN150 | |
| F | ASN150 | |
| G | ASN150 | |
| H | ASN150 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12235162, ECO:0007744|PDB:1LHR |
| Chain | Residue | Details |
| A | MET223 | |
| E | THR233 | |
| F | MET223 | |
| F | THR233 | |
| G | MET223 | |
| G | THR233 | |
| H | MET223 | |
| H | THR233 | |
| A | THR233 | |
| B | MET223 | |
| B | THR233 | |
| C | MET223 | |
| C | THR233 | |
| D | MET223 | |
| D | THR233 | |
| E | MET223 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | MOD_RES: N-acetylmethionine => ECO:0000269|PubMed:10395444 |
| Chain | Residue | Details |
| A | MET1 | |
| B | MET1 | |
| C | MET1 | |
| D | MET1 | |
| E | MET1 | |
| F | MET1 | |
| G | MET1 | |
| H | MET1 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 32 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O00764 |
| Chain | Residue | Details |
| A | SER59 | |
| C | SER164 | |
| C | SER213 | |
| C | SER285 | |
| D | SER59 | |
| D | SER164 | |
| D | SER213 | |
| D | SER285 | |
| E | SER59 | |
| E | SER164 | |
| E | SER213 | |
| A | SER164 | |
| E | SER285 | |
| F | SER59 | |
| F | SER164 | |
| F | SER213 | |
| F | SER285 | |
| G | SER59 | |
| G | SER164 | |
| G | SER213 | |
| G | SER285 | |
| H | SER59 | |
| A | SER213 | |
| H | SER164 | |
| H | SER213 | |
| H | SER285 | |
| A | SER285 | |
| B | SER59 | |
| B | SER164 | |
| B | SER213 | |
| B | SER285 | |
| C | SER59 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| A | GLY234 | |
| A | THR233 | |
| A | GLY232 | |
| A | ASP235 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| B | GLY234 | |
| B | THR233 | |
| B | GLY232 | |
| B | ASP235 |
| site_id | CSA3 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| C | GLY234 | |
| C | THR233 | |
| C | GLY232 | |
| C | ASP235 |
| site_id | CSA4 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| D | GLY234 | |
| D | THR233 | |
| D | GLY232 | |
| D | ASP235 |
| site_id | CSA5 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| E | GLY234 | |
| E | THR233 | |
| E | GLY232 | |
| E | ASP235 |
| site_id | CSA6 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| F | GLY234 | |
| F | THR233 | |
| F | GLY232 | |
| F | ASP235 |
| site_id | CSA7 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| G | GLY234 | |
| G | THR233 | |
| G | GLY232 | |
| G | ASP235 |
| site_id | CSA8 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1tz3 |
| Chain | Residue | Details |
| H | GLY234 | |
| H | THR233 | |
| H | GLY232 | |
| H | ASP235 |
