3LDW
Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004161 | molecular_function | dimethylallyltranstransferase activity |
| A | 0004337 | molecular_function | geranyltranstransferase activity |
| A | 0004659 | molecular_function | prenyltransferase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0008299 | biological_process | isoprenoid biosynthetic process |
| A | 0016020 | cellular_component | membrane |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016765 | molecular_function | transferase activity, transferring alkyl or aryl (other than methyl) groups |
| A | 0045337 | biological_process | farnesyl diphosphate biosynthetic process |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0004161 | molecular_function | dimethylallyltranstransferase activity |
| B | 0004337 | molecular_function | geranyltranstransferase activity |
| B | 0004659 | molecular_function | prenyltransferase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0008299 | biological_process | isoprenoid biosynthetic process |
| B | 0016020 | cellular_component | membrane |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016765 | molecular_function | transferase activity, transferring alkyl or aryl (other than methyl) groups |
| B | 0045337 | biological_process | farnesyl diphosphate biosynthetic process |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0004161 | molecular_function | dimethylallyltranstransferase activity |
| C | 0004337 | molecular_function | geranyltranstransferase activity |
| C | 0004659 | molecular_function | prenyltransferase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0008299 | biological_process | isoprenoid biosynthetic process |
| C | 0016020 | cellular_component | membrane |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016765 | molecular_function | transferase activity, transferring alkyl or aryl (other than methyl) groups |
| C | 0045337 | biological_process | farnesyl diphosphate biosynthetic process |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0004161 | molecular_function | dimethylallyltranstransferase activity |
| D | 0004337 | molecular_function | geranyltranstransferase activity |
| D | 0004659 | molecular_function | prenyltransferase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0008299 | biological_process | isoprenoid biosynthetic process |
| D | 0016020 | cellular_component | membrane |
| D | 0016740 | molecular_function | transferase activity |
| D | 0016765 | molecular_function | transferase activity, transferring alkyl or aryl (other than methyl) groups |
| D | 0045337 | biological_process | farnesyl diphosphate biosynthetic process |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE ZOL A 397 |
| Chain | Residue |
| A | ASP126 |
| A | IPE1101 |
| A | MG1102 |
| A | MG1103 |
| A | MG1104 |
| A | HOH1116 |
| A | HOH1117 |
| A | HOH1130 |
| A | HOH1142 |
| A | HOH1144 |
| A | HOH1155 |
| A | ASP130 |
| A | HOH1162 |
| A | HOH1164 |
| A | HOH1251 |
| A | ARG135 |
| A | GLN195 |
| A | LYS243 |
| A | THR244 |
| A | GLN284 |
| A | ASP287 |
| A | LYS301 |
| site_id | AC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE IPE A 1101 |
| Chain | Residue |
| A | GLY80 |
| A | LYS81 |
| A | ARG84 |
| A | GLN119 |
| A | ARG136 |
| A | TYR247 |
| A | PHE283 |
| A | GLN284 |
| A | ZOL397 |
| A | HOH1118 |
| A | HOH1119 |
| A | HOH1167 |
| A | HOH1190 |
| A | HOH1206 |
| A | HOH1250 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 1102 |
| Chain | Residue |
| A | ASP126 |
| A | ASP130 |
| A | ZOL397 |
| A | MG1103 |
| A | HOH1142 |
| A | HOH1164 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MG A 1103 |
| Chain | Residue |
| A | ASP126 |
| A | ASP130 |
| A | ZOL397 |
| A | MG1102 |
| A | HOH1130 |
| A | HOH1143 |
| A | HOH1161 |
| A | HOH1162 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 1104 |
| Chain | Residue |
| A | ASP287 |
| A | ZOL397 |
| A | HOH1116 |
| A | HOH1144 |
| A | HOH1251 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 1105 |
| Chain | Residue |
| A | GLU58 |
| A | GLU60 |
| A | HOH1152 |
| B | ASN232 |
| B | VAL235 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL A 1106 |
| Chain | Residue |
| A | GLY132 |
| A | GLU133 |
| A | LEU143 |
| B | ILE218 |
| site_id | AC8 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE ZOL B 397 |
| Chain | Residue |
| B | ASP126 |
| B | ASP130 |
| B | ARG135 |
| B | GLN195 |
| B | LYS243 |
| B | THR244 |
| B | GLN284 |
| B | ASP287 |
| B | LYS301 |
| B | IPE1101 |
| B | MG1102 |
| B | MG1103 |
| B | MG1104 |
| B | EDO1106 |
| B | HOH1135 |
| B | HOH1144 |
| B | HOH1149 |
| B | HOH1164 |
| B | HOH1186 |
| B | HOH1187 |
| B | HOH1261 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE IPE B 1101 |
| Chain | Residue |
| B | LYS81 |
| B | ARG84 |
| B | GLN119 |
| B | ARG136 |
| B | TYR247 |
| B | PHE283 |
| B | GLN284 |
| B | ZOL397 |
| B | HOH1136 |
| B | HOH1137 |
| B | HOH1193 |
| B | HOH1263 |
| B | HOH1268 |
| site_id | BC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MG B 1102 |
| Chain | Residue |
| B | ASP126 |
| B | ASP130 |
| B | ASP198 |
| B | ZOL397 |
| B | MG1104 |
| B | HOH1144 |
| B | HOH1145 |
| B | HOH1186 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 1103 |
| Chain | Residue |
| B | ASP287 |
| B | ZOL397 |
| B | HOH1135 |
| B | HOH1149 |
| B | HOH1164 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 1104 |
| Chain | Residue |
| B | ASP126 |
| B | ASP130 |
| B | ZOL397 |
| B | MG1102 |
| B | HOH1162 |
| B | HOH1187 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 1105 |
| Chain | Residue |
| B | LEU290 |
| B | ASP291 |
| B | GLY294 |
| B | SER296 |
| B | THR299 |
| B | LYS301 |
| B | GLY303 |
| B | EDO1106 |
| site_id | BC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO B 1106 |
| Chain | Residue |
| B | ASP291 |
| B | LYS301 |
| B | VAL302 |
| B | GLY303 |
| B | ZOL397 |
| B | GOL1105 |
| B | HOH1149 |
| B | HOH1164 |
| B | HOH1188 |
| site_id | BC6 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE ZOL C 397 |
| Chain | Residue |
| C | ASP126 |
| C | ASP130 |
| C | ARG135 |
| C | GLN195 |
| C | LYS243 |
| C | THR244 |
| C | GLN284 |
| C | ASP287 |
| C | LYS301 |
| C | IPE1101 |
| C | MG1102 |
| C | MG1103 |
| C | MG1104 |
| C | HOH1110 |
| C | HOH1120 |
| C | HOH1122 |
| C | HOH1167 |
| C | HOH1176 |
| C | HOH1191 |
| C | HOH1192 |
| site_id | BC7 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE IPE C 1101 |
| Chain | Residue |
| C | LYS81 |
| C | ARG84 |
| C | GLN119 |
| C | ARG136 |
| C | TYR247 |
| C | PHE283 |
| C | GLN284 |
| C | ZOL397 |
| C | HOH1121 |
| C | HOH1155 |
| C | HOH1162 |
| C | HOH1205 |
| C | HOH1211 |
| C | HOH1245 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 1102 |
| Chain | Residue |
| C | ASP126 |
| C | ASP130 |
| C | ZOL397 |
| C | MG1103 |
| C | HOH1118 |
| C | HOH1192 |
| site_id | BC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG C 1103 |
| Chain | Residue |
| C | ASP126 |
| C | ASP130 |
| C | ZOL397 |
| C | MG1102 |
| C | HOH1120 |
| C | HOH1122 |
| C | HOH1175 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG C 1104 |
| Chain | Residue |
| C | ASP287 |
| C | ZOL397 |
| C | HOH1110 |
| C | HOH1167 |
| C | HOH1191 |
| site_id | CC2 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE ZOL D 397 |
| Chain | Residue |
| D | ASP126 |
| D | ASP130 |
| D | ARG135 |
| D | GLN195 |
| D | LYS243 |
| D | THR244 |
| D | GLN284 |
| D | ASP287 |
| D | LYS301 |
| D | IPE1101 |
| D | MG1102 |
| D | MG1103 |
| D | MG1104 |
| D | HOH1157 |
| D | HOH1158 |
| D | HOH1159 |
| D | HOH1163 |
| D | HOH1200 |
| D | HOH1245 |
| D | HOH1264 |
| site_id | CC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE IPE D 1101 |
| Chain | Residue |
| D | LYS81 |
| D | ARG84 |
| D | GLN119 |
| D | ARG136 |
| D | TYR247 |
| D | PHE283 |
| D | GLN284 |
| D | ZOL397 |
| D | HOH1165 |
| D | HOH1218 |
| D | HOH1230 |
| D | HOH1251 |
| D | HOH1255 |
| site_id | CC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG D 1102 |
| Chain | Residue |
| D | ASP126 |
| D | ASP130 |
| D | ZOL397 |
| D | MG1103 |
| D | HOH1157 |
| D | HOH1160 |
| D | HOH1200 |
| site_id | CC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 1103 |
| Chain | Residue |
| D | ASP126 |
| D | ASP130 |
| D | ZOL397 |
| D | MG1102 |
| D | HOH1150 |
| D | HOH1158 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 1104 |
| Chain | Residue |
| D | ASP287 |
| D | ZOL397 |
| D | HOH1163 |
| D | HOH1196 |
| D | HOH1245 |
| site_id | CC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL D 1105 |
| Chain | Residue |
| B | LEU339 |
| B | LYS343 |
| D | ASP291 |
| D | ILE292 |
| D | ASP305 |
| D | ILE306 |
| D | ASP346 |
| D | HOH1164 |
Functional Information from PROSITE/UniProt
| site_id | PS00444 |
| Number of Residues | 13 |
| Details | POLYPRENYL_SYNTHASE_2 Polyprenyl synthases signature 2. MGeyFQIhDDYlD |
| Chain | Residue | Details |
| A | MET279-ASP291 |
