6V3M
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)
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 201 |
| Chain | Residue |
| A | ASP10 |
| A | HIS12 |
| A | HIS44 |
| A | QOG202 |
| site_id | AC2 |
| Number of Residues | 18 |
| Details | binding site for residue QOG A 202 |
| Chain | Residue |
| A | ILE59 |
| A | GLY60 |
| A | PHE63 |
| A | SER64 |
| A | ASP65 |
| A | PHE70 |
| A | LEU78 |
| A | ZN201 |
| A | HOH355 |
| A | HOH392 |
| B | LYS134 |
| B | HOH317 |
| B | HOH338 |
| A | ASP10 |
| A | HIS12 |
| A | HIS36 |
| A | SER37 |
| A | HIS44 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | binding site for residue DMS A 203 |
| Chain | Residue |
| A | ALA102 |
| A | GLN103 |
| A | PRO105 |
| A | LYS106 |
| A | LEU107 |
| A | LYS134 |
| A | THR135 |
| A | HOH391 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue DMS A 204 |
| Chain | Residue |
| A | ASP123 |
| A | LEU124 |
| A | PRO125 |
| A | HOH330 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 205 |
| Chain | Residue |
| A | ALA92 |
| A | ILE93 |
| A | LEU122 |
| A | ASP123 |
| A | HOH305 |
| A | HOH394 |
| site_id | AC6 |
| Number of Residues | 11 |
| Details | binding site for residue MLT A 206 |
| Chain | Residue |
| A | GLY140 |
| A | TYR141 |
| A | ARG144 |
| A | HOH326 |
| B | GLY140 |
| B | TYR141 |
| B | HOH378 |
| C | ARG69 |
| C | GLY140 |
| C | TYR141 |
| C | ARG144 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 201 |
| Chain | Residue |
| B | ASP10 |
| B | HIS12 |
| B | HIS44 |
| B | QOG202 |
| site_id | AC8 |
| Number of Residues | 12 |
| Details | binding site for residue QOG B 202 |
| Chain | Residue |
| B | ASP10 |
| B | HIS12 |
| B | SER37 |
| B | HIS44 |
| B | ILE59 |
| B | GLY60 |
| B | PHE63 |
| B | PHE70 |
| B | ZN201 |
| B | HOH364 |
| C | LYS134 |
| C | HOH320 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue DMS B 203 |
| Chain | Residue |
| B | ALA102 |
| B | GLN103 |
| B | PRO105 |
| B | LYS106 |
| B | LEU107 |
| B | LYS134 |
| B | THR135 |
| B | HOH313 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue DMS B 204 |
| Chain | Residue |
| A | ALA87 |
| A | GLN88 |
| A | GLY90 |
| A | HOH438 |
| B | LEU124 |
| B | PRO125 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 205 |
| Chain | Residue |
| B | ALA92 |
| B | ILE93 |
| B | LEU122 |
| B | ASP123 |
| B | LEU124 |
| B | HOH304 |
| B | HOH334 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 201 |
| Chain | Residue |
| C | ASP10 |
| C | HIS12 |
| C | HIS44 |
| C | QOG202 |
| site_id | AD4 |
| Number of Residues | 14 |
| Details | binding site for residue QOG C 202 |
| Chain | Residue |
| C | HIS44 |
| C | ILE59 |
| C | PHE63 |
| C | PHE70 |
| C | LEU78 |
| C | ZN201 |
| C | HOH360 |
| A | LYS134 |
| A | GLU137 |
| A | HOH308 |
| A | HOH332 |
| C | ASP10 |
| C | HIS12 |
| C | SER37 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue DMS C 203 |
| Chain | Residue |
| C | ALA102 |
| C | GLN103 |
| C | PRO105 |
| C | LYS106 |
| C | LEU107 |
| C | LYS134 |
| C | THR135 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 204 |
| Chain | Residue |
| C | ASP123 |
| C | LEU124 |
| C | PRO125 |
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 | ASP40 | |
| A | ALA102 | |
| A | ALA133 | |
| B | ASP40 | |
| B | ALA102 | |
| B | ALA133 | |
| C | ASP40 | |
| 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 |
