3Q8H
Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008299 | biological_process | isoprenoid biosynthetic process |
| A | 0008685 | molecular_function | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity |
| A | 0016114 | biological_process | terpenoid biosynthetic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0008299 | biological_process | isoprenoid biosynthetic process |
| B | 0008685 | molecular_function | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity |
| B | 0016114 | biological_process | terpenoid biosynthetic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0008299 | biological_process | isoprenoid biosynthetic process |
| C | 0008685 | molecular_function | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity |
| C | 0016114 | biological_process | terpenoid biosynthetic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| C | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 163 |
| Chain | Residue |
| A | ASP10 |
| A | HIS12 |
| A | HIS44 |
| B | HOH166 |
| site_id | AC2 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE AO9 A 165 |
| Chain | Residue |
| A | HOH169 |
| A | HOH171 |
| A | HOH180 |
| A | HOH209 |
| B | ALA102 |
| B | PRO105 |
| B | LYS106 |
| B | LEU107 |
| B | ALA108 |
| B | ALA133 |
| B | LYS134 |
| B | HOH166 |
| A | HIS36 |
| A | ASP58 |
| A | ILE59 |
| A | GLY60 |
| A | PHE63 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE K A 170 |
| Chain | Residue |
| A | HOH285 |
| B | HOH286 |
| C | HOH287 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 172 |
| Chain | Residue |
| A | ALA120 |
| A | ASP121 |
| A | HOH224 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 173 |
| Chain | Residue |
| A | ALA92 |
| A | ILE93 |
| A | LEU122 |
| A | ASP123 |
| A | HOH259 |
| site_id | AC6 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE AO9 A 164 |
| Chain | Residue |
| A | ALA102 |
| A | PRO105 |
| A | LYS106 |
| A | LEU107 |
| A | ALA108 |
| A | ALA133 |
| A | LYS134 |
| A | THR135 |
| A | HOH195 |
| A | HOH266 |
| A | HOH293 |
| C | HIS36 |
| C | ASP58 |
| C | ILE59 |
| C | GLY60 |
| C | ARG61 |
| C | PHE63 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 163 |
| Chain | Residue |
| B | ASP10 |
| B | HIS12 |
| B | HIS44 |
| B | HOH291 |
| site_id | AC8 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE AO9 B 165 |
| Chain | Residue |
| B | HIS36 |
| B | ASP58 |
| B | ILE59 |
| B | GLY60 |
| B | ARG61 |
| B | PHE63 |
| B | LEU78 |
| B | HOH175 |
| B | HOH178 |
| B | HOH290 |
| B | HOH291 |
| C | ALA102 |
| C | PRO105 |
| C | LYS106 |
| C | LEU107 |
| C | ALA108 |
| C | ALA133 |
| C | LYS134 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 163 |
| Chain | Residue |
| A | HOH195 |
| C | ASP10 |
| C | HIS12 |
| C | HIS44 |
Functional Information from PROSITE/UniProt
| site_id | PS01350 |
| Number of Residues | 16 |
| Details | ISPF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. SDADVLlHAitDAlfG |
| Chain | Residue | Details |
| A | SER37-GLY52 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 21 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00107 |
| Chain | Residue | Details |
| A | ASP10 | |
| B | HIS36 | |
| B | HIS44 | |
| B | ASP58 | |
| B | PHE63 | |
| B | ARG144 | |
| C | ASP10 | |
| C | HIS12 | |
| C | HIS36 | |
| C | HIS44 | |
| C | ASP58 | |
| A | HIS12 | |
| C | PHE63 | |
| C | ARG144 | |
| A | HIS36 | |
| A | HIS44 | |
| A | ASP58 | |
| A | PHE63 | |
| A | ARG144 | |
| B | ASP10 | |
| B | HIS12 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 9 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ASP67 | |
| A | ALA102 | |
| A | ALA133 | |
| B | ASP67 | |
| B | ALA102 | |
| B | ALA133 | |
| C | ASP67 | |
| C | ALA102 | |
| C | ALA133 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | SITE: Transition state stabilizer => ECO:0000255|HAMAP-Rule:MF_00107 |
| Chain | Residue | Details |
| A | HIS36 | |
| A | THR135 | |
| B | HIS36 | |
| B | THR135 | |
| C | HIS36 | |
| C | THR135 |
