3DAQ
Crystal structure of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008700 | molecular_function | 4-hydroxy-2-oxoglutarate aldolase activity |
| A | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0009436 | biological_process | glyoxylate catabolic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019877 | biological_process | diaminopimelate biosynthetic process |
| A | 0044281 | biological_process | small molecule metabolic process |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008700 | molecular_function | 4-hydroxy-2-oxoglutarate aldolase activity |
| B | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| B | 0009436 | biological_process | glyoxylate catabolic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019877 | biological_process | diaminopimelate biosynthetic process |
| B | 0044281 | biological_process | small molecule metabolic process |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0008700 | molecular_function | 4-hydroxy-2-oxoglutarate aldolase activity |
| C | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
| C | 0009085 | biological_process | lysine biosynthetic process |
| C | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| C | 0009436 | biological_process | glyoxylate catabolic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0019877 | biological_process | diaminopimelate biosynthetic process |
| C | 0044281 | biological_process | small molecule metabolic process |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0008700 | molecular_function | 4-hydroxy-2-oxoglutarate aldolase activity |
| D | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
| D | 0009085 | biological_process | lysine biosynthetic process |
| D | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| D | 0009436 | biological_process | glyoxylate catabolic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0019877 | biological_process | diaminopimelate biosynthetic process |
| D | 0044281 | biological_process | small molecule metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL D 1 |
| Chain | Residue |
| D | THR13 |
| D | PRO15 |
| D | HIS29 |
| D | HOH340 |
| D | HOH372 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL C 294 |
| Chain | Residue |
| C | HOH365 |
| C | THR13 |
| C | PRO15 |
| C | HIS29 |
| C | HOH341 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 294 |
| Chain | Residue |
| A | THR13 |
| A | PRO15 |
| A | HIS29 |
| A | HOH327 |
| A | HOH340 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL B 294 |
| Chain | Residue |
| B | THR13 |
| B | PRO15 |
| B | HIS29 |
| B | HOH337 |
| B | HOH343 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL D 294 |
| Chain | Residue |
| D | TYR135 |
| D | ARG140 |
| D | LYS163 |
| D | ALA165 |
| D | GLY189 |
| D | ASN249 |
| D | HOH389 |
| D | HOH436 |
| D | HOH476 |
| D | HOH731 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 295 |
| Chain | Residue |
| B | TYR135 |
| B | ARG140 |
| B | LYS163 |
| B | GLY189 |
| B | ASN249 |
| B | HOH385 |
| B | HOH431 |
| B | HOH493 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL C 295 |
| Chain | Residue |
| C | TYR135 |
| C | ARG140 |
| C | LYS163 |
| C | ALA165 |
| C | GLY189 |
| C | ASN249 |
| C | HOH373 |
| C | HOH396 |
| site_id | AC8 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 295 |
| Chain | Residue |
| A | TYR135 |
| A | ARG140 |
| A | LYS163 |
| A | ALA165 |
| A | GLY189 |
| A | ASN249 |
| A | HOH389 |
| A | HOH447 |
| A | HOH484 |
| A | HOH656 |
| site_id | AC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL C 296 |
| Chain | Residue |
| C | ASN44 |
| C | GLY45 |
| C | THR46 |
| C | SER50 |
| C | GLY78 |
| C | GLY80 |
| C | MET103 |
| C | LEU104 |
| C | ILE105 |
| D | TYR109 |
| site_id | BC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL C 297 |
| Chain | Residue |
| B | ASP168 |
| B | GLU170 |
| B | TYR171 |
| C | GLN199 |
| C | GLN224 |
| C | GLY227 |
| C | LEU228 |
| C | ASP229 |
| C | HOH374 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL D 295 |
| Chain | Residue |
| C | TYR109 |
| D | ASN44 |
| D | GLY45 |
| D | THR46 |
| D | SER50 |
| D | GLY80 |
| D | MET103 |
| D | LEU104 |
| D | ILE105 |
| site_id | BC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL A 296 |
| Chain | Residue |
| A | ASN44 |
| A | GLY45 |
| A | THR46 |
| A | SER50 |
| A | GLY78 |
| A | GLY80 |
| A | MET103 |
| A | LEU104 |
| A | ILE105 |
| A | HOH732 |
| B | TYR109 |
| site_id | BC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL B 296 |
| Chain | Residue |
| B | SER50 |
| B | GLY78 |
| B | GLY80 |
| B | MET103 |
| B | LEU104 |
| B | ILE105 |
| B | TYR135 |
| A | TYR109 |
| B | ASN44 |
| B | GLY45 |
| B | THR46 |
Functional Information from PROSITE/UniProt
| site_id | PS00666 |
| Number of Residues | 31 |
| Details | DHDPS_2 Dihydrodipicolinate synthase signature 2. YNVPsrTnmtIepetveilsqhpy.IvALKDA |
| Chain | Residue | Details |
| A | TYR135-ALA165 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_00418 |
| Chain | Residue | Details |
| A | TYR135 | |
| B | TYR135 | |
| C | TYR135 | |
| D | TYR135 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Schiff-base intermediate with substrate => ECO:0000255|HAMAP-Rule:MF_00418 |
| Chain | Residue | Details |
| A | LYS163 | |
| B | LYS163 | |
| C | LYS163 | |
| D | LYS163 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00418 |
| Chain | Residue | Details |
| A | THR47 | |
| C | THR47 | |
| C | ILE206 | |
| D | THR47 | |
| D | ILE206 | |
| A | ILE206 | |
| B | THR47 | |
| B | ILE206 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | SITE: Part of a proton relay during catalysis => ECO:0000255|HAMAP-Rule:MF_00418 |
| Chain | Residue | Details |
| C | THR46 | |
| C | TYR109 | |
| D | THR46 | |
| D | TYR109 | |
| A | THR46 | |
| A | TYR109 | |
| B | THR46 | |
| B | TYR109 |
