1M5W
1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008615 | biological_process | pyridoxine biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| A | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| A | 0042802 | molecular_function | identical protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008615 | biological_process | pyridoxine biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| B | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| B | 0042802 | molecular_function | identical protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0008615 | biological_process | pyridoxine biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| C | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| C | 0042802 | molecular_function | identical protein binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0008615 | biological_process | pyridoxine biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| D | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| D | 0042802 | molecular_function | identical protein binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0005829 | cellular_component | cytosol |
| E | 0008615 | biological_process | pyridoxine biosynthetic process |
| E | 0016740 | molecular_function | transferase activity |
| E | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| E | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| E | 0042802 | molecular_function | identical protein binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0005829 | cellular_component | cytosol |
| F | 0008615 | biological_process | pyridoxine biosynthetic process |
| F | 0016740 | molecular_function | transferase activity |
| F | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| F | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| F | 0042802 | molecular_function | identical protein binding |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0005829 | cellular_component | cytosol |
| G | 0008615 | biological_process | pyridoxine biosynthetic process |
| G | 0016740 | molecular_function | transferase activity |
| G | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| G | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| G | 0042802 | molecular_function | identical protein binding |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0005829 | cellular_component | cytosol |
| H | 0008615 | biological_process | pyridoxine biosynthetic process |
| H | 0016740 | molecular_function | transferase activity |
| H | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
| H | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
| H | 0042802 | molecular_function | identical protein binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE DXP A 1001 |
| Chain | Residue |
| A | ASN9 |
| A | HIS193 |
| A | PO41101 |
| A | HOH1146 |
| A | HOH1158 |
| E | ARG20 |
| E | HOH1020 |
| A | ASP11 |
| A | HIS12 |
| A | HIS45 |
| A | ARG47 |
| A | GLU72 |
| A | THR102 |
| A | THR103 |
| A | GLU153 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE DXP B 1002 |
| Chain | Residue |
| B | ASN9 |
| B | ASP11 |
| B | HIS45 |
| B | HIS52 |
| B | GLU72 |
| B | HIS193 |
| B | GLY215 |
| B | HIS216 |
| B | HOH1071 |
| G | HOH1071 |
| site_id | AC3 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE DXP C 1003 |
| Chain | Residue |
| C | ASP11 |
| C | HIS12 |
| C | HIS45 |
| C | HIS52 |
| C | GLU72 |
| C | THR102 |
| C | THR103 |
| C | HIS193 |
| C | PO41103 |
| C | HOH1145 |
| C | HOH1194 |
| C | HOH1195 |
| C | HOH1197 |
| F | ARG20 |
| F | HOH1099 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE DXP E 1005 |
| Chain | Residue |
| A | ARG20 |
| E | ASP11 |
| E | HIS45 |
| E | HIS52 |
| E | GLU72 |
| E | LYS97 |
| E | HIS193 |
| E | GLY215 |
| E | HIS216 |
| E | HOH1058 |
| site_id | AC5 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DXP F 1006 |
| Chain | Residue |
| C | ARG20 |
| F | ASN9 |
| F | ASP11 |
| F | HIS45 |
| F | ARG47 |
| F | HIS52 |
| F | GLU72 |
| F | HIS193 |
| F | GLY215 |
| F | HIS216 |
| F | HOH1043 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE DXP G 1007 |
| Chain | Residue |
| B | ARG20 |
| G | ASN9 |
| G | ASP11 |
| G | HIS45 |
| G | ARG51 |
| G | HIS52 |
| G | GLU72 |
| G | HIS193 |
| G | GLY194 |
| G | GLY215 |
| G | HIS216 |
| G | HOH1106 |
| G | HOH1107 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE PO4 A 1101 |
| Chain | Residue |
| A | HIS193 |
| A | GLY194 |
| A | ILE214 |
| A | GLY215 |
| A | HIS216 |
| A | DXP1001 |
| A | HOH1120 |
| A | HOH1139 |
| A | HOH1146 |
| E | ARG20 |
| site_id | AC8 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE PO4 C 1103 |
| Chain | Residue |
| C | HIS193 |
| C | GLY194 |
| C | ILE214 |
| C | GLY215 |
| C | HIS216 |
| C | DXP1003 |
| C | HOH1118 |
| C | HOH1145 |
| C | HOH1194 |
| F | ARG20 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 16 |
| Details | ACT_SITE: Proton acceptor |
| Chain | Residue | Details |
| A | LEU46 | |
| E | MET73 | |
| F | LEU46 | |
| F | MET73 | |
| G | LEU46 | |
| G | MET73 | |
| H | LEU46 | |
| H | MET73 | |
| A | MET73 | |
| B | LEU46 | |
| B | MET73 | |
| C | LEU46 | |
| C | MET73 | |
| D | LEU46 | |
| D | MET73 | |
| E | LEU46 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton donor |
| Chain | Residue | Details |
| A | GLY194 | |
| B | GLY194 | |
| C | GLY194 | |
| D | GLY194 | |
| E | GLY194 | |
| F | GLY194 | |
| G | GLY194 | |
| H | GLY194 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 64 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ILE10 | |
| B | HIS12 | |
| B | GLY21 | |
| B | GLU48 | |
| B | ILE53 | |
| B | THR103 | |
| B | LEU195 | |
| B | HIS216 | |
| C | ILE10 | |
| C | HIS12 | |
| C | GLY21 | |
| A | HIS12 | |
| C | GLU48 | |
| C | ILE53 | |
| C | THR103 | |
| C | LEU195 | |
| C | HIS216 | |
| D | ILE10 | |
| D | HIS12 | |
| D | GLY21 | |
| D | GLU48 | |
| D | ILE53 | |
| A | GLY21 | |
| D | THR103 | |
| D | LEU195 | |
| D | HIS216 | |
| E | ILE10 | |
| E | HIS12 | |
| E | GLY21 | |
| E | GLU48 | |
| E | ILE53 | |
| E | THR103 | |
| E | LEU195 | |
| A | GLU48 | |
| E | HIS216 | |
| F | ILE10 | |
| F | HIS12 | |
| F | GLY21 | |
| F | GLU48 | |
| F | ILE53 | |
| F | THR103 | |
| F | LEU195 | |
| F | HIS216 | |
| G | ILE10 | |
| A | ILE53 | |
| G | HIS12 | |
| G | GLY21 | |
| G | GLU48 | |
| G | ILE53 | |
| G | THR103 | |
| G | LEU195 | |
| G | HIS216 | |
| H | ILE10 | |
| H | HIS12 | |
| H | GLY21 | |
| A | THR103 | |
| H | GLU48 | |
| H | ILE53 | |
| H | THR103 | |
| H | LEU195 | |
| H | HIS216 | |
| A | LEU195 | |
| A | HIS216 | |
| B | ILE10 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | SITE: Transition state stabilizer |
| Chain | Residue | Details |
| A | ILE154 | |
| B | ILE154 | |
| C | ILE154 | |
| D | ILE154 | |
| E | ILE154 | |
| F | ILE154 | |
| G | ILE154 | |
| H | ILE154 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| A | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| A | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| A | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| A | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| A | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| A | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| A | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| B | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| B | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| B | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| B | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| B | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| B | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| B | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA3 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| C | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| C | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| C | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| C | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| C | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| C | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| C | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| C | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| C | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA4 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| D | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| D | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| D | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| D | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| D | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| D | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| D | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| D | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| D | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA5 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| E | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| E | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| E | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| E | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| E | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| E | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| E | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| E | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| E | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA6 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| F | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| F | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| F | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| F | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| F | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| F | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| F | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| F | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| F | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA7 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| G | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| G | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| G | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| G | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| G | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| G | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| G | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| G | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| G | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA8 |
| Number of Residues | 9 |
| Details | M-CSA 243 |
| Chain | Residue | Details |
| H | ILE10 | electrostatic stabiliser, hydrogen bond donor |
| H | ILE13 | attractive charge-charge interaction, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| H | LEU46 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| H | GLU48 | attractive charge-charge interaction, electrostatic stabiliser, increase acidity, increase basicity |
| H | HIS52 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase acidity, increase basicity |
| H | MET73 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| H | GLU104 | electrostatic stabiliser, hydrogen bond acceptor |
| H | ILE154 | electrostatic stabiliser, hydrogen bond acceptor |
| H | GLY194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
