6NMO
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4
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 | 6 |
Details | binding site for residue ZN A 201 |
Chain | Residue |
A | ASP10 |
A | HIS12 |
A | HIS44 |
A | MLI203 |
A | HOH304 |
A | HOH315 |
site_id | AC2 |
Number of Residues | 8 |
Details | binding site for residue DMS A 202 |
Chain | Residue |
A | LYS106 |
A | LEU107 |
A | LYS134 |
A | THR135 |
A | HOH332 |
A | ALA102 |
A | GLN103 |
A | PRO105 |
site_id | AC3 |
Number of Residues | 11 |
Details | binding site for residue MLI A 203 |
Chain | Residue |
A | HIS12 |
A | GLY35 |
A | HIS36 |
A | SER37 |
A | HIS44 |
A | ZN201 |
A | HOH304 |
A | HOH315 |
A | HOH327 |
A | HOH385 |
B | HOH367 |
site_id | AC4 |
Number of Residues | 13 |
Details | binding site for residue MLI B 201 |
Chain | Residue |
A | GLY140 |
A | TYR141 |
A | ARG144 |
B | GLY140 |
B | TYR141 |
B | ARG144 |
B | HOH322 |
B | HOH344 |
B | HOH351 |
B | HOH378 |
B | HOH401 |
C | TYR141 |
C | ARG144 |
site_id | AC5 |
Number of Residues | 6 |
Details | binding site for residue ZN B 202 |
Chain | Residue |
B | ASP10 |
B | HIS12 |
B | HIS44 |
B | HOH308 |
C | HOH306 |
C | HOH425 |
site_id | AC6 |
Number of Residues | 5 |
Details | binding site for residue EDO B 203 |
Chain | Residue |
B | LYS106 |
B | LEU107 |
B | ALA108 |
B | HOH315 |
B | HOH336 |
site_id | AC7 |
Number of Residues | 3 |
Details | binding site for residue EDO B 204 |
Chain | Residue |
B | HOH328 |
B | HOH389 |
C | ALA108 |
site_id | AC8 |
Number of Residues | 12 |
Details | binding site for residue MLI B 205 |
Chain | Residue |
A | TYR9 |
A | TYR141 |
A | GLU149 |
B | TYR9 |
B | GLU149 |
B | HOH309 |
B | HOH311 |
B | HOH317 |
C | TYR9 |
C | TYR141 |
C | LEU142 |
C | GLU149 |
site_id | AC9 |
Number of Residues | 5 |
Details | binding site for residue ZN C 201 |
Chain | Residue |
C | ASP10 |
C | HIS12 |
C | HIS44 |
C | QMS202 |
C | HOH325 |
site_id | AD1 |
Number of Residues | 13 |
Details | binding site for residue QMS C 202 |
Chain | Residue |
A | LYS134 |
A | GLU137 |
C | ASP10 |
C | HIS12 |
C | LEU34 |
C | GLY35 |
C | HIS36 |
C | ALA39 |
C | HIS44 |
C | ILE59 |
C | ZN201 |
C | HOH325 |
C | HOH356 |
site_id | AD2 |
Number of Residues | 5 |
Details | binding site for residue EDO C 203 |
Chain | Residue |
C | LYS106 |
C | LEU107 |
C | ALA108 |
C | HOH311 |
C | HOH367 |
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 |