5ESS
Crystal Structure of M. tuberculosis MenD bound to Mg2+ and covalent intermediate I (a ThDP and decarboxylated 2-oxoglutarate adduct)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0009234 | biological_process | menaquinone biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0030976 | molecular_function | thiamine pyrophosphate binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0009234 | biological_process | menaquinone biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0030976 | molecular_function | thiamine pyrophosphate binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0005886 | cellular_component | plasma membrane |
| C | 0009234 | biological_process | menaquinone biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0030145 | molecular_function | manganese ion binding |
| C | 0030976 | molecular_function | thiamine pyrophosphate binding |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0005886 | cellular_component | plasma membrane |
| D | 0009234 | biological_process | menaquinone biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0030145 | molecular_function | manganese ion binding |
| D | 0030976 | molecular_function | thiamine pyrophosphate binding |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 601 |
| Chain | Residue |
| A | ASP440 |
| A | ASP469 |
| A | GLY471 |
| A | DPO606 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 602 |
| Chain | Residue |
| A | GLU140 |
| A | ALA142 |
| A | PRO143 |
| A | THR146 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue FMT A 603 |
| Chain | Residue |
| A | ARG394 |
| A | VAL395 |
| A | ARG396 |
| A | HOH752 |
| A | THR250 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 604 |
| Chain | Residue |
| A | LEU347 |
| A | ALA348 |
| A | HIS350 |
| A | HIS357 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue FMT A 605 |
| Chain | Residue |
| A | GLY28 |
| A | SER29 |
| A | ARG30 |
| A | THR78 |
| A | GLN118 |
| A | HOH770 |
| D | TOG601 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | binding site for residue DPO A 606 |
| Chain | Residue |
| A | ASN378 |
| A | GLY439 |
| A | ASP440 |
| A | LEU441 |
| A | THR442 |
| A | ASP469 |
| A | GLY471 |
| A | GLY473 |
| A | MG601 |
| A | HOH739 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue FMT B 601 |
| Chain | Residue |
| B | GLU140 |
| B | ALA142 |
| B | THR146 |
| B | TRP153 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue FMT B 602 |
| Chain | Residue |
| B | THR250 |
| B | ILE393 |
| B | VAL395 |
| B | ARG396 |
| B | HOH710 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue FMT B 603 |
| Chain | Residue |
| B | GLY28 |
| B | SER29 |
| B | ARG30 |
| B | THR78 |
| B | GLN118 |
| B | HOH840 |
| C | TOG601 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 604 |
| Chain | Residue |
| B | THR245 |
| B | ALA247 |
| B | ARG253 |
| B | PRO258 |
| B | LEU259 |
| site_id | AD2 |
| Number of Residues | 30 |
| Details | binding site for residue TOG C 601 |
| Chain | Residue |
| B | PRO27 |
| B | GLU55 |
| B | THR78 |
| B | THR81 |
| B | ALA82 |
| B | ASN117 |
| B | GLN118 |
| B | FMT603 |
| C | ALA376 |
| C | SER377 |
| C | ASN378 |
| C | PRO379 |
| C | ARG381 |
| C | ARG399 |
| C | ALA402 |
| C | GLY403 |
| C | ILE404 |
| C | ASP405 |
| C | GLY439 |
| C | ASP440 |
| C | LEU441 |
| C | THR442 |
| C | ASP469 |
| C | GLY471 |
| C | GLY472 |
| C | GLY473 |
| C | ILE474 |
| C | MG602 |
| C | HOH730 |
| C | HOH781 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 602 |
| Chain | Residue |
| C | ASP440 |
| C | ASP469 |
| C | GLY471 |
| C | TOG601 |
| C | HOH730 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue FMT C 603 |
| Chain | Residue |
| C | THR250 |
| C | VAL395 |
| C | ARG396 |
| C | HOH732 |
| site_id | AD5 |
| Number of Residues | 2 |
| Details | binding site for residue FMT C 604 |
| Chain | Residue |
| C | ARG396 |
| C | HOH767 |
| site_id | AD6 |
| Number of Residues | 30 |
| Details | binding site for residue TOG D 601 |
| Chain | Residue |
| A | THR81 |
| A | ALA82 |
| A | ASN117 |
| A | GLN118 |
| A | FMT605 |
| D | ALA376 |
| D | SER377 |
| D | ASN378 |
| D | PRO379 |
| D | ARG381 |
| D | ARG399 |
| D | ALA402 |
| D | GLY403 |
| D | ILE404 |
| D | ASP405 |
| D | GLY439 |
| D | ASP440 |
| D | LEU441 |
| D | THR442 |
| D | ASP469 |
| D | GLY471 |
| D | GLY472 |
| D | GLY473 |
| D | ILE474 |
| D | MG602 |
| D | HOH719 |
| D | HOH755 |
| A | PRO27 |
| A | GLU55 |
| A | THR78 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 602 |
| Chain | Residue |
| D | ASP440 |
| D | ASP469 |
| D | GLY471 |
| D | TOG601 |
| D | HOH719 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue FMT D 603 |
| Chain | Residue |
| D | THR245 |
| D | ALA247 |
| D | LEU259 |
| D | HOH805 |
| site_id | AD9 |
| Number of Residues | 2 |
| Details | binding site for residue ACT D 604 |
| Chain | Residue |
| D | VAL395 |
| D | HOH704 |
| site_id | AE1 |
| Number of Residues | 1 |
| Details | binding site for residue ACT D 605 |
| Chain | Residue |
| D | ALA538 |
