6MWK
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0883
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 | 5 |
Details | binding site for residue ZN A 201 |
Chain | Residue |
A | ASP10 |
A | HIS12 |
A | HIS44 |
A | K4Y202 |
A | HOH304 |
site_id | AC2 |
Number of Residues | 16 |
Details | binding site for residue K4Y A 202 |
Chain | Residue |
A | SER37 |
A | HIS44 |
A | ILE59 |
A | GLY60 |
A | PHE63 |
A | SER64 |
A | ASP65 |
A | PHE70 |
A | LEU78 |
A | ZN201 |
A | HOH304 |
B | LYS134 |
A | ASP10 |
A | HIS12 |
A | GLY35 |
A | HIS36 |
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 | HOH306 |
site_id | AC4 |
Number of Residues | 5 |
Details | binding site for residue DMS A 204 |
Chain | Residue |
A | ALA87 |
A | GLN88 |
B | ASP123 |
B | LEU124 |
B | PRO125 |
site_id | AC5 |
Number of Residues | 7 |
Details | binding site for residue MG A 205 |
Chain | Residue |
A | HOH340 |
A | HOH349 |
A | HOH403 |
B | HOH381 |
B | HOH410 |
C | HOH369 |
C | HOH376 |
site_id | AC6 |
Number of Residues | 4 |
Details | binding site for residue ZN B 201 |
Chain | Residue |
B | ASP10 |
B | HIS12 |
B | HIS44 |
B | K4Y202 |
site_id | AC7 |
Number of Residues | 12 |
Details | binding site for residue K4Y B 202 |
Chain | Residue |
B | ASP10 |
B | HIS12 |
B | GLY35 |
B | HIS36 |
B | HIS44 |
B | ILE59 |
B | PHE63 |
B | LEU78 |
B | ZN201 |
B | HOH312 |
B | HOH387 |
C | LYS134 |
site_id | AC8 |
Number of Residues | 6 |
Details | binding site for residue DMS B 203 |
Chain | Residue |
B | ALA102 |
B | PRO105 |
B | LYS106 |
B | LEU107 |
B | ALA108 |
B | HOH304 |
site_id | AC9 |
Number of Residues | 13 |
Details | binding site for residue MLA B 204 |
Chain | Residue |
A | GLY140 |
A | TYR141 |
A | ARG144 |
B | GLY140 |
B | TYR141 |
B | ARG144 |
B | HOH309 |
B | HOH342 |
B | HOH349 |
B | HOH352 |
B | HOH398 |
C | TYR141 |
C | ARG144 |
site_id | AD1 |
Number of Residues | 4 |
Details | binding site for residue ZN C 200 |
Chain | Residue |
C | ASP10 |
C | HIS12 |
C | HIS44 |
C | K4Y201 |
site_id | AD2 |
Number of Residues | 10 |
Details | binding site for residue K4Y C 201 |
Chain | Residue |
A | LYS134 |
C | ASP10 |
C | HIS12 |
C | GLY35 |
C | HIS36 |
C | HIS44 |
C | PHE63 |
C | ZN200 |
C | HOH343 |
C | HOH393 |
site_id | AD3 |
Number of Residues | 7 |
Details | binding site for residue DMS C 202 |
Chain | Residue |
C | ALA102 |
C | PRO105 |
C | LYS106 |
C | LEU107 |
C | LYS134 |
C | THR135 |
C | HOH304 |
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 |