3KEU
Crystal Structure of Human PL Kinase with bound PLP and ATP
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 | ATP407 |
A | MPD512 |
A | HOH792 |
A | HOH806 |
site_id | AC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG A 401 |
Chain | Residue |
A | ASP235 |
A | ATP407 |
A | PLP500 |
site_id | AC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NA A 402 |
Chain | Residue |
A | THR148 |
A | THR186 |
A | ATP407 |
A | HOH656 |
A | ASP113 |
site_id | AC4 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE ATP A 407 |
Chain | Residue |
A | ASP113 |
A | ASP118 |
A | ASN150 |
A | GLU153 |
A | THR186 |
A | SER187 |
A | VAL201 |
A | ARG224 |
A | LYS225 |
A | VAL226 |
A | ALA228 |
A | THR233 |
A | GLY234 |
A | LEU267 |
A | MG400 |
A | MG401 |
A | NA402 |
A | PLP500 |
A | MPD512 |
A | HOH792 |
A | HOH805 |
A | HOH806 |
A | HOH824 |
A | HOH849 |
site_id | AC5 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE PLP A 500 |
Chain | Residue |
A | SER12 |
A | VAL19 |
A | GLY20 |
A | THR47 |
A | VAL231 |
A | GLY232 |
A | THR233 |
A | GLY234 |
A | ASP235 |
A | MG401 |
A | ATP407 |
site_id | AC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MPD A 508 |
Chain | Residue |
A | SER12 |
A | THR47 |
A | TYR84 |
site_id | AC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MPD A 512 |
Chain | Residue |
A | ASP118 |
A | LEU199 |
A | MG400 |
A | ATP407 |
A | HOH822 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MPD A 516 |
Chain | Residue |
A | LYS76 |
A | ASP78 |
A | ASN105 |
A | HOH907 |
site_id | AC9 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE SO4 A 524 |
Chain | Residue |
A | GLU155 |
site_id | BC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 528 |
Chain | Residue |
A | GLN63 |
A | ARG70 |
A | MET93 |
A | GLU100 |
site_id | BC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 538 |
Chain | Residue |
A | CYS5 |
A | LEU31 |
A | GLY32 |
A | LYS247 |
site_id | BC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG B 404 |
Chain | Residue |
B | ASP118 |
B | ATP409 |
B | MPD514 |
B | HOH797 |
B | HOH798 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG B 405 |
Chain | Residue |
B | VAL115 |
B | ASP235 |
B | ATP409 |
B | PLP500 |
site_id | BC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE NA B 406 |
Chain | Residue |
B | ASP113 |
B | THR148 |
B | PRO149 |
B | ASN150 |
B | THR186 |
B | ATP409 |
B | HOH796 |
site_id | BC6 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE ATP B 409 |
Chain | Residue |
B | LEU263 |
B | LEU267 |
B | MG404 |
B | MG405 |
B | NA406 |
B | PLP500 |
B | MPD514 |
B | HOH766 |
B | HOH797 |
B | HOH846 |
B | ASP113 |
B | ASP118 |
B | TYR127 |
B | ASN150 |
B | GLU153 |
B | THR186 |
B | SER187 |
B | VAL201 |
B | ARG224 |
B | LYS225 |
B | VAL226 |
B | ALA228 |
B | THR233 |
B | GLY234 |
site_id | BC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MPD B 508 |
Chain | Residue |
B | SER12 |
B | VAL19 |
B | HIS46 |
B | THR47 |
B | VAL231 |
site_id | BC8 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE PLP B 500 |
Chain | Residue |
B | SER12 |
B | VAL19 |
B | GLY20 |
B | THR47 |
B | PHE230 |
B | VAL231 |
B | GLY232 |
B | THR233 |
B | GLY234 |
B | ASP235 |
B | MG405 |
B | ATP409 |
site_id | BC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MPD B 510 |
Chain | Residue |
B | ASP181 |
B | ARG206 |
B | ARG207 |
B | ARG208 |
B | HOH842 |
site_id | CC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MPD B 514 |
Chain | Residue |
B | ASP118 |
B | LYS225 |
B | MG404 |
B | ATP409 |
B | HOH798 |
B | HOH884 |
site_id | CC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MPD B 518 |
Chain | Residue |
B | SER177 |
B | LEU312 |
B | MPD520 |
B | HOH785 |
site_id | CC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MPD B 520 |
Chain | Residue |
B | ASP173 |
B | SER177 |
B | ARG206 |
B | LEU312 |
B | MPD518 |
B | HOH785 |
site_id | CC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MPD B 522 |
Chain | Residue |
B | GLN165 |
site_id | CC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 B 526 |
Chain | Residue |
B | GLN63 |
B | GLU100 |
site_id | CC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 B 530 |
Chain | Residue |
B | GLU4 |
B | CYS5 |
B | ASP78 |
B | HIS246 |
B | HOH869 |
site_id | CC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 B 532 |
Chain | Residue |
B | GLU155 |
B | ARG160 |
site_id | CC8 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 534 |
Chain | Residue |
B | LEU31 |
B | GLY32 |
B | HIS246 |
site_id | CC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 B 536 |
Chain | Residue |
B | TYR84 |
B | HOH896 |
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 | 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 |
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 |