3FHX
Crystal structure of D235A mutant of 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 | 0016310 | biological_process | phosphorylation |
| 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 | 0016310 | biological_process | phosphorylation |
| 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 | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 400 |
| Chain | Residue |
| A | ASP118 |
| A | SO4315 |
| A | HOH389 |
| A | HOH390 |
| A | ATP407 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE NA A 402 |
| Chain | Residue |
| A | THR186 |
| A | HOH392 |
| A | ATP407 |
| A | ASP113 |
| A | THR148 |
| A | PRO149 |
| A | ASN150 |
| site_id | AC3 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE ATP A 407 |
| Chain | Residue |
| A | ASP113 |
| A | ASP118 |
| A | TYR127 |
| A | ASN150 |
| A | GLU153 |
| A | THR186 |
| A | SER187 |
| A | ARG224 |
| A | LYS225 |
| A | VAL226 |
| A | ALA228 |
| A | THR233 |
| A | LEU267 |
| A | SO4314 |
| A | SO4315 |
| A | HOH349 |
| A | HOH389 |
| A | HOH390 |
| A | HOH392 |
| A | MG400 |
| A | NA402 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PXL A 313 |
| Chain | Residue |
| A | SER12 |
| A | HIS46 |
| A | THR47 |
| A | VAL231 |
| A | SO4314 |
| A | HOH342 |
| A | HOH367 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 314 |
| Chain | Residue |
| A | VAL231 |
| A | GLY232 |
| A | GLY234 |
| A | ALA235 |
| A | PXL313 |
| A | HOH342 |
| A | ATP407 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 315 |
| Chain | Residue |
| A | LEU199 |
| A | HOH390 |
| A | MG400 |
| A | ATP407 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 316 |
| Chain | Residue |
| A | ARG70 |
| A | MET93 |
| A | GLU100 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 A 317 |
| Chain | Residue |
| A | GLU3 |
| A | GLU4 |
| A | CYS5 |
| A | ASP78 |
| A | HIS246 |
| A | HOH383 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 A 318 |
| Chain | Residue |
| A | GLY32 |
| A | LYS247 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 319 |
| Chain | Residue |
| A | ASP145 |
| A | GLY179 |
| A | ASP181 |
| A | MPD321 |
| A | HOH334 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 320 |
| Chain | Residue |
| A | VAL56 |
| A | GLU61 |
| A | HOH340 |
| B | GLU61 |
| B | GLU280 |
| site_id | BC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MPD A 321 |
| Chain | Residue |
| A | ASP181 |
| A | SO4319 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 404 |
| Chain | Residue |
| B | ASP118 |
| B | SO4315 |
| B | HOH344 |
| B | HOH383 |
| B | ATP409 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE NA B 406 |
| Chain | Residue |
| B | ASP113 |
| B | THR148 |
| B | PRO149 |
| B | ASN150 |
| B | GLU153 |
| B | THR186 |
| B | HOH385 |
| B | ATP409 |
| site_id | BC6 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE ATP B 409 |
| Chain | Residue |
| B | THR233 |
| B | LEU263 |
| B | LEU267 |
| B | PLP314 |
| B | SO4315 |
| B | HOH344 |
| B | HOH353 |
| B | MG404 |
| B | NA406 |
| B | ASP113 |
| B | ASP118 |
| B | TYR127 |
| B | ASN150 |
| B | GLU153 |
| B | THR186 |
| B | SER187 |
| B | LEU199 |
| B | ARG224 |
| B | LYS225 |
| B | VAL226 |
| B | ALA228 |
| site_id | BC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PXL B 313 |
| Chain | Residue |
| B | SER12 |
| B | VAL19 |
| B | PHE43 |
| B | ASN45 |
| B | HIS46 |
| B | THR47 |
| B | GLY48 |
| B | VAL231 |
| B | PLP314 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PLP B 314 |
| Chain | Residue |
| B | VAL231 |
| B | GLY232 |
| B | THR233 |
| B | GLY234 |
| B | PXL313 |
| B | HOH384 |
| B | ATP409 |
| site_id | BC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 315 |
| Chain | Residue |
| B | HOH359 |
| B | MG404 |
| B | ATP409 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 316 |
| Chain | Residue |
| B | GLN63 |
| B | ARG70 |
| B | GLU100 |
| site_id | CC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 317 |
| Chain | Residue |
| B | ALA144 |
| B | ASP145 |
| B | GLY179 |
| B | ASP181 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 318 |
| Chain | Residue |
| B | GLN165 |
| B | HOH351 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MPD B 319 |
| Chain | Residue |
| A | ARG170 |
| B | GLY124 |
| B | GLU130 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MPD B 320 |
| Chain | Residue |
| B | ASP173 |
| B | SER177 |
| B | LEU312 |
| site_id | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MPD B 321 |
| Chain | Residue |
| B | ASP181 |
| B | ARG206 |
| B | ARG208 |
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 | ALA235 | |
| B | ALA235 |
| 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 | 2 |
| Details | MOD_RES: N-acetylmethionine => ECO:0000250|UniProtKB:P82197 |
| Chain | Residue | Details |
| A | MET1 | |
| B | MET1 |
| site_id | SWS_FT_FI12 |
| 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_FI13 |
| 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_FI14 |
| 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 |
