2AJP
Crystal structure of a human pyridoxal kinase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| 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 | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| A | 0016301 | molecular_function | kinase 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 | 0034774 | cellular_component | secretory granule lumen |
| A | 0035580 | cellular_component | specific granule lumen |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0042816 | biological_process | vitamin B6 metabolic process |
| 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 |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005634 | cellular_component | nucleus |
| 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 | 0009443 | biological_process | pyridoxal 5'-phosphate salvage |
| B | 0016301 | molecular_function | kinase 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 | 0034774 | cellular_component | secretory granule lumen |
| B | 0035580 | cellular_component | specific granule lumen |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0042816 | biological_process | vitamin B6 metabolic process |
| 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 |
| B | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 401 |
| Chain | Residue |
| A | ASP118 |
| A | ANP501 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG B 1401 |
| Chain | Residue |
| B | ASP118 |
| B | ANP1501 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 402 |
| Chain | Residue |
| A | GLY232 |
| A | THR233 |
| A | GLY234 |
| A | ANP501 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 403 |
| Chain | Residue |
| A | GLU34 |
| A | ASP36 |
| B | ARG16 |
| A | ARG6 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX B 404 |
| Chain | Residue |
| A | ASP36 |
| B | ARG16 |
| B | GLY17 |
| B | TYR18 |
| B | ARG22 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 405 |
| Chain | Residue |
| A | THR82 |
| A | GLY83 |
| A | ASP113 |
| A | TYR136 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE UNX A 406 |
| Chain | Residue |
| A | VAL14 |
| A | ARG16 |
| A | GLY17 |
| A | ASN45 |
| A | HIS46 |
| A | GLU290 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE UNX A 407 |
| Chain | Residue |
| A | HIS264 |
| A | GLN268 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 408 |
| Chain | Residue |
| A | GLN11 |
| A | GLY83 |
| A | TYR84 |
| A | ASP235 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX B 409 |
| Chain | Residue |
| A | TYR18 |
| A | VAL294 |
| B | GLN29 |
| B | PHE33 |
| B | ILE35 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 410 |
| Chain | Residue |
| A | ARG22 |
| A | THR25 |
| A | PHE26 |
| B | GLN29 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX B 411 |
| Chain | Residue |
| A | GLN29 |
| A | VAL30 |
| A | GLY32 |
| B | VAL294 |
| B | LYS297 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE UNX B 412 |
| Chain | Residue |
| A | ASP36 |
| A | ALA37 |
| B | HIS13 |
| B | VAL14 |
| B | ILE15 |
| B | ARG22 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE UNX A 413 |
| Chain | Residue |
| A | ASN75 |
| A | LYS76 |
| A | TYR77 |
| A | LEU101 |
| A | ASN105 |
| A | LEU108 |
| site_id | BC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX A 414 |
| Chain | Residue |
| A | PRO142 |
| A | ALA144 |
| A | GLY179 |
| site_id | BC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE UNX A 415 |
| Chain | Residue |
| A | GLN165 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 416 |
| Chain | Residue |
| A | HIS46 |
| A | PRO286 |
| A | LEU289 |
| A | GLU290 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 417 |
| Chain | Residue |
| A | TYR18 |
| A | VAL231 |
| A | GLU290 |
| A | LEU291 |
| site_id | CC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE UNX A 418 |
| Chain | Residue |
| A | PRO249 |
| A | ASN250 |
| site_id | CC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE UNX A 419 |
| Chain | Residue |
| A | LEU199 |
| A | LYS225 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE UNX A 420 |
| Chain | Residue |
| A | PHE33 |
| A | HIS246 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX A 421 |
| Chain | Residue |
| A | ASP113 |
| A | THR148 |
| A | THR186 |
| A | GLY234 |
| A | ANP501 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX B 1402 |
| Chain | Residue |
| B | GLY232 |
| B | THR233 |
| B | GLY234 |
| B | ASP235 |
| B | ANP1501 |
| site_id | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1403 |
| Chain | Residue |
| B | ARG6 |
| B | GLU34 |
| B | ASP36 |
| site_id | CC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 1404 |
| Chain | Residue |
| A | GLY17 |
| A | TYR18 |
| A | ARG22 |
| B | ASP36 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX B 1405 |
| Chain | Residue |
| B | THR82 |
| B | GLY83 |
| B | CYS112 |
| B | ASP113 |
| B | TYR136 |
| site_id | CC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE UNX B 1406 |
| Chain | Residue |
| B | VAL14 |
| B | ARG16 |
| B | GLY17 |
| B | ASN45 |
| B | HIS46 |
| B | GLU290 |
| site_id | DC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX B 1408 |
| Chain | Residue |
| B | GLN11 |
| B | GLY83 |
| B | TYR84 |
| B | ASP235 |
| site_id | DC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX A 1409 |
| Chain | Residue |
| A | GLN29 |
| A | ILE35 |
| B | TYR18 |
| B | ARG22 |
| B | VAL294 |
| site_id | DC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX B 1410 |
| Chain | Residue |
| B | ASN21 |
| B | ARG22 |
| B | THR25 |
| B | PHE26 |
| site_id | DC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE UNX A 1411 |
| Chain | Residue |
| A | VAL294 |
| A | LYS297 |
| B | GLN29 |
| B | VAL30 |
| site_id | DC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE UNX A 1412 |
| Chain | Residue |
| A | HIS13 |
| A | VAL14 |
| A | ILE15 |
| A | ARG22 |
| B | ASP36 |
| B | ALA37 |
| site_id | DC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE UNX B 1413 |
| Chain | Residue |
| B | ASN75 |
| B | LYS76 |
| B | TYR77 |
| B | LEU101 |
| B | ASN105 |
| B | LEU108 |
| site_id | DC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1414 |
| Chain | Residue |
| B | PRO142 |
| B | ALA144 |
| B | ASP145 |
| site_id | DC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1415 |
| Chain | Residue |
| B | SER164 |
| B | GLN165 |
| B | PRO191 |
| site_id | DC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1416 |
| Chain | Residue |
| B | VAL231 |
| B | LEU289 |
| B | UNX1417 |
| site_id | EC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE UNX B 1417 |
| Chain | Residue |
| B | TYR18 |
| B | VAL231 |
| B | GLU290 |
| B | LEU291 |
| B | UNX1416 |
| site_id | EC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1418 |
| Chain | Residue |
| B | HIS248 |
| B | PRO249 |
| B | ASN250 |
| site_id | EC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE UNX B 1419 |
| Chain | Residue |
| B | LEU199 |
| site_id | EC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1420 |
| Chain | Residue |
| B | LEU31 |
| B | PHE33 |
| B | LYS247 |
| site_id | EC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE UNX B 1421 |
| Chain | Residue |
| B | THR148 |
| B | THR186 |
| B | ANP1501 |
| site_id | EC6 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE ANP A 501 |
| Chain | Residue |
| A | ASP113 |
| A | ASP118 |
| A | ASN150 |
| A | GLU153 |
| A | THR186 |
| A | SER187 |
| A | VAL201 |
| A | VAL226 |
| A | ALA228 |
| A | PHE230 |
| A | THR233 |
| A | GLY234 |
| A | PHE237 |
| A | LEU267 |
| A | MG401 |
| A | UNX402 |
| A | UNX421 |
| site_id | EC7 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE ANP B 1501 |
| Chain | Residue |
| B | ASP113 |
| B | VAL115 |
| B | ASP118 |
| B | ASN150 |
| B | GLU153 |
| B | THR186 |
| B | SER187 |
| B | LEU199 |
| B | VAL201 |
| B | LYS225 |
| B | VAL226 |
| B | ALA228 |
| B | PHE230 |
| B | THR233 |
| B | MG1401 |
| B | UNX1402 |
| B | UNX1421 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000305|PubMed:19351586 |
| Chain | Residue | Details |
| A | ASP235 | |
| B | ASP235 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19351586, ECO:0007744|PDB:3FHX |
| Chain | Residue | Details |
| A | SER12 | |
| B | SER12 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|Ref.16, ECO:0007744|PDB:3KEU |
| Chain | Residue | Details |
| A | THR47 | |
| B | THR47 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19351586, ECO:0000269|PubMed:22879864, ECO:0007744|PDB:3FHX, ECO:0007744|PDB:4EN4 |
| Chain | Residue | Details |
| A | ASP113 | |
| B | ASP113 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17766369, ECO:0000269|PubMed:19351586, ECO:0000269|PubMed:22879864, ECO:0000269|Ref.16, ECO:0007744|PDB:3FHX, ECO:0007744|PDB:3KEU, ECO:0007744|PDB:4EN4 |
| Chain | Residue | Details |
| A | ASP118 | |
| B | ASP118 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17766369, ECO:0000269|PubMed:19351586, ECO:0000269|PubMed:22879864, ECO:0000269|Ref.16, ECO:0007744|PDB:2YXT, ECO:0007744|PDB:3FHX, ECO:0007744|PDB:3KEU, ECO:0007744|PDB:4EN4 |
| Chain | Residue | Details |
| A | THR148 | |
| A | THR186 | |
| B | THR148 | |
| B | THR186 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19351586, ECO:0000269|Ref.16, ECO:0007744|PDB:3FHY, ECO:0007744|PDB:3KEU |
| Chain | Residue | Details |
| A | ASN150 | |
| B | ASN150 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22879864, ECO:0000269|Ref.16, ECO:0007744|PDB:3KEU, ECO:0007744|PDB:4EN4 |
| Chain | Residue | Details |
| A | VAL226 | |
| B | VAL226 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17766369, ECO:0000269|PubMed:19351586, ECO:0000269|PubMed:22879864, ECO:0000269|Ref.16, ECO:0007744|PDB:2YXU, ECO:0007744|PDB:3FHX, ECO:0007744|PDB:3FHY, ECO:0007744|PDB:3KEU, ECO:0007744|PDB:4EN4 |
| Chain | Residue | Details |
| A | THR233 | |
| B | THR233 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19351586, ECO:0000269|Ref.16, ECO:0007744|PDB:3FHX, ECO:0007744|PDB:3KEU |
| Chain | Residue | Details |
| A | GLY234 | |
| B | GLY234 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19369195 |
| Chain | Residue | Details |
| A | SER59 | |
| A | SER164 | |
| B | SER59 | |
| B | SER164 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19369195 |
| Chain | Residue | Details |
| A | SER213 | |
| B | SER213 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19369195, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER285 | |
| B | SER285 |
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 |
