3KEU
Crystal Structure of Human PL Kinase with bound PLP and ATP
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 | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| 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 | 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 | 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 | 0042822 | biological_process | pyridoxal phosphate metabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000166 | molecular_function | nucleotide binding |
| 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 | 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 | 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 | 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 | 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 | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"2YXT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"2YXU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
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 |
