5EJM
ThDP-Mn2+ complex of R413A variant of EcMenD soaked with 2-ketoglutarate for 35 min
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003824 | molecular_function | catalytic activity |
| 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 | 0042803 | molecular_function | protein homodimerization activity |
| A | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0003824 | molecular_function | catalytic activity |
| 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 | 0042803 | molecular_function | protein homodimerization activity |
| B | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0003824 | molecular_function | catalytic activity |
| 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 | 0042803 | molecular_function | protein homodimerization activity |
| C | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0003824 | molecular_function | catalytic activity |
| 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 | 0042803 | molecular_function | protein homodimerization activity |
| D | 0044281 | biological_process | small molecule metabolic process |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| E | 0000287 | molecular_function | magnesium ion binding |
| E | 0003824 | molecular_function | catalytic activity |
| E | 0009234 | biological_process | menaquinone biosynthetic process |
| E | 0016740 | molecular_function | transferase activity |
| E | 0030145 | molecular_function | manganese ion binding |
| E | 0030976 | molecular_function | thiamine pyrophosphate binding |
| E | 0042803 | molecular_function | protein homodimerization activity |
| E | 0044281 | biological_process | small molecule metabolic process |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| F | 0000287 | molecular_function | magnesium ion binding |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0009234 | biological_process | menaquinone biosynthetic process |
| F | 0016740 | molecular_function | transferase activity |
| F | 0030145 | molecular_function | manganese ion binding |
| F | 0030976 | molecular_function | thiamine pyrophosphate binding |
| F | 0042803 | molecular_function | protein homodimerization activity |
| F | 0044281 | biological_process | small molecule metabolic process |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| G | 0000287 | molecular_function | magnesium ion binding |
| G | 0003824 | molecular_function | catalytic activity |
| G | 0009234 | biological_process | menaquinone biosynthetic process |
| G | 0016740 | molecular_function | transferase activity |
| G | 0030145 | molecular_function | manganese ion binding |
| G | 0030976 | molecular_function | thiamine pyrophosphate binding |
| G | 0042803 | molecular_function | protein homodimerization activity |
| G | 0044281 | biological_process | small molecule metabolic process |
| G | 0046872 | molecular_function | metal ion binding |
| G | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| H | 0000287 | molecular_function | magnesium ion binding |
| H | 0003824 | molecular_function | catalytic activity |
| H | 0009234 | biological_process | menaquinone biosynthetic process |
| H | 0016740 | molecular_function | transferase activity |
| H | 0030145 | molecular_function | manganese ion binding |
| H | 0030976 | molecular_function | thiamine pyrophosphate binding |
| H | 0042803 | molecular_function | protein homodimerization activity |
| H | 0044281 | biological_process | small molecule metabolic process |
| H | 0046872 | molecular_function | metal ion binding |
| H | 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 | 31 |
| Details | binding site for residue TD5 A 601 |
| Chain | Residue |
| A | SER391 |
| A | SER444 |
| A | TYR447 |
| A | ASN469 |
| A | GLY471 |
| A | GLY472 |
| A | GLN473 |
| A | ILE474 |
| A | MN602 |
| A | HOH833 |
| A | HOH851 |
| A | LEU392 |
| A | HOH961 |
| A | HOH970 |
| B | PRO30 |
| B | GLY31 |
| B | SER32 |
| B | ARG33 |
| B | GLU55 |
| B | THR78 |
| B | THR81 |
| B | ALA82 |
| A | SER416 |
| B | ARG107 |
| B | GLN118 |
| A | GLY417 |
| A | ILE418 |
| A | ASP419 |
| A | GLY441 |
| A | ASP442 |
| A | LEU443 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MN A 602 |
| Chain | Residue |
| A | ASP442 |
| A | ASN469 |
| A | GLY471 |
| A | TD5601 |
| A | HOH833 |
| site_id | AC3 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 603 |
| Chain | Residue |
| A | HIS49 |
| A | HIS50 |
| A | THR51 |
| A | ARG430 |
| A | LEU454 |
| A | GLN457 |
| A | HOH768 |
| A | HOH819 |
| A | HOH902 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 604 |
| Chain | Residue |
| A | ARG364 |
| A | HIS374 |
| A | ASP378 |
| site_id | AC5 |
| Number of Residues | 31 |
| Details | binding site for residue TD5 B 601 |
| Chain | Residue |
| A | PRO30 |
| A | GLY31 |
| A | SER32 |
| A | ARG33 |
| A | GLU55 |
| A | THR78 |
| A | THR81 |
| A | ARG107 |
| A | GLN118 |
| B | SER391 |
| B | LEU392 |
| B | SER416 |
| B | GLY417 |
| B | ILE418 |
| B | ASP419 |
| B | GLY441 |
| B | ASP442 |
| B | LEU443 |
| B | SER444 |
| B | TYR447 |
| B | ASN469 |
| B | GLY471 |
| B | GLY472 |
| B | GLN473 |
| B | ILE474 |
| B | MN602 |
| B | HOH743 |
| B | HOH747 |
| B | HOH767 |
| B | HOH826 |
| B | HOH951 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue MN B 602 |
| Chain | Residue |
| B | ASP442 |
| B | ASN469 |
| B | GLY471 |
| B | TD5601 |
| B | HOH747 |
| site_id | AC7 |
| Number of Residues | 9 |
| Details | binding site for residue GOL B 603 |
| Chain | Residue |
| B | HIS49 |
| B | HIS50 |
| B | THR51 |
| B | ARG430 |
| B | LEU454 |
| B | GLN457 |
| B | HOH736 |
| B | HOH941 |
| B | HOH991 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 604 |
| Chain | Residue |
| B | ARG364 |
| B | HIS374 |
| B | ASP378 |
| site_id | AC9 |
| Number of Residues | 32 |
| Details | binding site for residue TD5 C 601 |
| Chain | Residue |
| C | GLY417 |
| C | ILE418 |
| C | ASP419 |
| C | GLY441 |
| C | ASP442 |
| C | LEU443 |
| C | SER444 |
| C | TYR447 |
| C | ASN469 |
| C | GLY471 |
| C | GLY472 |
| C | GLN473 |
| C | ILE474 |
| C | MN602 |
| C | HOH721 |
| C | HOH734 |
| C | HOH824 |
| C | HOH923 |
| C | HOH950 |
| D | PRO30 |
| D | GLY31 |
| D | SER32 |
| D | ARG33 |
| D | GLU55 |
| D | THR78 |
| D | THR81 |
| D | ALA82 |
| D | ARG107 |
| D | GLN118 |
| C | SER391 |
| C | LEU392 |
| C | SER416 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue MN C 602 |
| Chain | Residue |
| C | ASP442 |
| C | ASN469 |
| C | GLY471 |
| C | TD5601 |
| C | HOH734 |
| site_id | AD2 |
| Number of Residues | 8 |
| Details | binding site for residue GOL C 603 |
| Chain | Residue |
| C | HIS49 |
| C | HIS50 |
| C | THR51 |
| C | ARG430 |
| C | LEU454 |
| C | GLN457 |
| C | HOH705 |
| C | HOH887 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 604 |
| Chain | Residue |
| C | ARG364 |
| C | HIS374 |
| C | CYS377 |
| C | ASP378 |
| site_id | AD4 |
| Number of Residues | 32 |
| Details | binding site for residue TD5 D 601 |
| Chain | Residue |
| C | PRO30 |
| C | GLY31 |
| C | SER32 |
| C | ARG33 |
| C | GLU55 |
| C | THR78 |
| C | THR81 |
| C | ALA82 |
| C | ARG107 |
| C | GLN118 |
| C | HOH937 |
| D | SER391 |
| D | LEU392 |
| D | SER416 |
| D | GLY417 |
| D | ILE418 |
| D | ASP419 |
| D | GLY441 |
| D | ASP442 |
| D | LEU443 |
| D | SER444 |
| D | TYR447 |
| D | ASN469 |
| D | GLY471 |
| D | GLY472 |
| D | GLN473 |
| D | ILE474 |
| D | MN602 |
| D | HOH702 |
| D | HOH787 |
| D | HOH899 |
| D | HOH999 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue MN D 602 |
| Chain | Residue |
| D | ASP442 |
| D | ASN469 |
| D | GLY471 |
| D | TD5601 |
| D | HOH787 |
| site_id | AD6 |
| Number of Residues | 9 |
| Details | binding site for residue GOL D 603 |
| Chain | Residue |
| D | HIS49 |
| D | HIS50 |
| D | THR51 |
| D | ARG430 |
| D | LEU454 |
| D | GLN457 |
| D | HOH719 |
| D | HOH808 |
| D | HOH1082 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 604 |
| Chain | Residue |
| D | ARG364 |
| D | HIS374 |
| D | ASP378 |
| D | HOH976 |
| site_id | AD8 |
| Number of Residues | 31 |
| Details | binding site for residue TD5 E 601 |
| Chain | Residue |
| E | SER391 |
| E | LEU392 |
| E | SER416 |
| E | GLY417 |
| E | ILE418 |
| E | ASP419 |
| E | GLY441 |
| E | ASP442 |
| E | LEU443 |
| E | SER444 |
| E | TYR447 |
| E | ASN469 |
| E | GLY471 |
| E | GLY472 |
| E | GLN473 |
| E | ILE474 |
| E | MN602 |
| E | HOH710 |
| E | HOH747 |
| E | HOH818 |
| E | HOH919 |
| F | PRO30 |
| F | GLY31 |
| F | SER32 |
| F | ARG33 |
| F | GLU55 |
| F | THR78 |
| F | THR81 |
| F | ARG107 |
| F | GLN118 |
| F | HOH981 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue MN E 602 |
| Chain | Residue |
| E | ASP442 |
| E | ASN469 |
| E | GLY471 |
| E | TD5601 |
| E | HOH818 |
| site_id | AE1 |
| Number of Residues | 9 |
| Details | binding site for residue GOL E 603 |
| Chain | Residue |
| E | HIS49 |
| E | HIS50 |
| E | THR51 |
| E | ARG430 |
| E | LEU454 |
| E | GLN457 |
| E | HOH778 |
| E | HOH900 |
| E | HOH1043 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO E 604 |
| Chain | Residue |
| E | ARG364 |
| E | HIS374 |
| E | ASP378 |
| site_id | AE3 |
| Number of Residues | 32 |
| Details | binding site for residue TD5 F 601 |
| Chain | Residue |
| E | PRO30 |
| E | GLY31 |
| E | SER32 |
| E | ARG33 |
| E | GLU55 |
| E | THR78 |
| E | THR81 |
| E | ALA82 |
| E | ARG107 |
| E | GLN118 |
| F | SER391 |
| F | LEU392 |
| F | SER416 |
| F | GLY417 |
| F | ILE418 |
| F | ASP419 |
| F | GLY441 |
| F | ASP442 |
| F | LEU443 |
| F | SER444 |
| F | TYR447 |
| F | ASN469 |
| F | GLY471 |
| F | GLY472 |
| F | GLN473 |
| F | ILE474 |
| F | MN602 |
| F | HOH713 |
| F | HOH734 |
| F | HOH746 |
| F | HOH873 |
| F | HOH915 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue MN F 602 |
| Chain | Residue |
| F | ASP442 |
| F | ASN469 |
| F | GLY471 |
| F | TD5601 |
| F | HOH746 |
| site_id | AE5 |
| Number of Residues | 9 |
| Details | binding site for residue GOL F 603 |
| Chain | Residue |
| F | HIS49 |
| F | HIS50 |
| F | THR51 |
| F | ARG430 |
| F | LEU454 |
| F | GLN457 |
| F | HOH733 |
| F | HOH848 |
| F | HOH974 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO F 604 |
| Chain | Residue |
| F | ARG364 |
| F | HIS374 |
| F | ARG375 |
| F | ASP378 |
| F | HOH1052 |
| site_id | AE7 |
| Number of Residues | 32 |
| Details | binding site for residue TD5 G 601 |
| Chain | Residue |
| G | SER391 |
| G | LEU392 |
| G | SER416 |
| G | GLY417 |
| G | ILE418 |
| G | ASP419 |
| G | GLY441 |
| G | ASP442 |
| G | LEU443 |
| G | SER444 |
| G | TYR447 |
| G | ASN469 |
| G | GLY471 |
| G | GLY472 |
| G | GLN473 |
| G | ILE474 |
| G | MN602 |
| G | HOH701 |
| G | HOH780 |
| G | HOH806 |
| G | HOH945 |
| H | PRO30 |
| H | GLY31 |
| H | SER32 |
| H | ARG33 |
| H | GLU55 |
| H | THR78 |
| H | THR81 |
| H | ALA82 |
| H | ARG107 |
| H | GLN118 |
| H | HOH927 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue MN G 602 |
| Chain | Residue |
| G | ASP442 |
| G | ASN469 |
| G | GLY471 |
| G | TD5601 |
| G | HOH806 |
| site_id | AE9 |
| Number of Residues | 9 |
| Details | binding site for residue GOL G 603 |
| Chain | Residue |
| G | HIS49 |
| G | HIS50 |
| G | THR51 |
| G | ARG430 |
| G | LEU454 |
| G | GLN457 |
| G | HOH758 |
| G | HOH844 |
| G | HOH1050 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO G 604 |
| Chain | Residue |
| G | ARG364 |
| G | HIS374 |
| G | ARG375 |
| G | ASP378 |
| G | HOH872 |
| site_id | AF2 |
| Number of Residues | 32 |
| Details | binding site for residue TD5 H 601 |
| Chain | Residue |
| G | PRO30 |
| G | GLY31 |
| G | SER32 |
| G | ARG33 |
| G | GLU55 |
| G | THR78 |
| G | THR81 |
| G | ALA82 |
| G | ARG107 |
| G | GLN118 |
| H | SER391 |
| H | LEU392 |
| H | SER416 |
| H | GLY417 |
| H | ILE418 |
| H | ASP419 |
| H | GLY441 |
| H | ASP442 |
| H | LEU443 |
| H | SER444 |
| H | TYR447 |
| H | ASN469 |
| H | GLY471 |
| H | GLY472 |
| H | GLN473 |
| H | ILE474 |
| H | MN602 |
| H | HOH712 |
| H | HOH759 |
| H | HOH866 |
| H | HOH874 |
| H | HOH885 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue MN H 602 |
| Chain | Residue |
| H | ASP442 |
| H | ASN469 |
| H | GLY471 |
| H | TD5601 |
| H | HOH759 |
| site_id | AF4 |
| Number of Residues | 9 |
| Details | binding site for residue GOL H 603 |
| Chain | Residue |
| H | HIS49 |
| H | HIS50 |
| H | THR51 |
| H | ARG430 |
| H | LEU454 |
| H | GLN457 |
| H | HOH713 |
| H | HOH946 |
| H | HOH998 |
| site_id | AF5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO H 604 |
| Chain | Residue |
| H | ARG364 |
| H | HIS374 |
| H | ASP378 |
