5Z2U
ThDP-Mn2+ complex of R395A variant of EcMenD soaked with 2-ketoglutarate for 5 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 | 29 |
| Details | binding site for residue TD6 A 601 |
| Chain | Residue |
| A | SER391 |
| A | SER444 |
| A | TYR447 |
| A | ASN469 |
| A | GLY471 |
| A | GLY472 |
| A | GLN473 |
| A | ILE474 |
| A | MG602 |
| A | HOH791 |
| A | HOH818 |
| A | LEU392 |
| A | HOH875 |
| H | PRO30 |
| H | GLY31 |
| H | SER32 |
| H | ARG33 |
| H | GLU55 |
| H | THR78 |
| H | ALA82 |
| H | GLN118 |
| H | HOH943 |
| A | SER416 |
| A | GLY417 |
| A | ILE418 |
| A | ASP419 |
| A | GLY441 |
| A | ASP442 |
| A | LEU443 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 602 |
| Chain | Residue |
| A | ASP442 |
| A | ASN469 |
| A | GLY471 |
| A | TD6601 |
| A | HOH818 |
| site_id | AC3 |
| Number of Residues | 31 |
| Details | binding site for residue TD6 B 601 |
| Chain | Residue |
| B | SER391 |
| B | LEU392 |
| B | SER416 |
| B | GLY417 |
| B | ILE418 |
| B | ASP419 |
| B | GLY441 |
| B | ASP442 |
| B | LEU443 |
| B | SER444 |
| B | ASN469 |
| B | GLY471 |
| B | GLY472 |
| B | GLN473 |
| B | ILE474 |
| B | PHE475 |
| B | MG602 |
| B | HOH720 |
| B | HOH898 |
| G | PRO30 |
| G | GLY31 |
| G | SER32 |
| G | ARG33 |
| G | GLU55 |
| G | THR78 |
| G | THR81 |
| G | ALA82 |
| G | ARG107 |
| G | GLN118 |
| G | HOH701 |
| G | HOH962 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 602 |
| Chain | Residue |
| B | ASP442 |
| B | ASN469 |
| B | GLY471 |
| B | TD6601 |
| B | HOH728 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue FMT B 603 |
| Chain | Residue |
| B | LYS70 |
| B | ARG228 |
| B | MET229 |
| B | SER230 |
| B | HOH878 |
| B | HOH1007 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue FMT B 604 |
| Chain | Residue |
| B | GLN187 |
| B | TRP193 |
| B | HOH984 |
| B | HOH1012 |
| site_id | AC7 |
| Number of Residues | 33 |
| Details | binding site for residue TD6 C 601 |
| Chain | Residue |
| C | HOH808 |
| C | HOH826 |
| D | PRO30 |
| D | GLY31 |
| D | SER32 |
| D | ARG33 |
| D | GLU55 |
| D | THR78 |
| D | THR81 |
| D | ALA82 |
| D | ARG107 |
| D | ASN117 |
| D | GLN118 |
| D | HOH1015 |
| C | SER391 |
| C | LEU392 |
| C | ARG413 |
| C | SER416 |
| C | GLY417 |
| C | ILE418 |
| C | ASP419 |
| C | GLY441 |
| C | ASP442 |
| C | LEU443 |
| C | SER444 |
| C | ASN469 |
| C | GLY471 |
| C | GLY472 |
| C | GLN473 |
| C | ILE474 |
| C | MG602 |
| C | HOH748 |
| C | HOH766 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 602 |
| Chain | Residue |
| C | ASP442 |
| C | ASN469 |
| C | GLY471 |
| C | TD6601 |
| C | HOH766 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 603 |
| Chain | Residue |
| C | HIS49 |
| C | HIS50 |
| C | THR51 |
| C | ARG430 |
| C | LEU454 |
| C | HOH701 |
| C | HOH795 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue FMT C 604 |
| Chain | Residue |
| C | ALA241 |
| C | GLN242 |
| C | TRP246 |
| C | HOH928 |
| site_id | AD2 |
| Number of Residues | 27 |
| Details | binding site for residue TD6 D 601 |
| Chain | Residue |
| C | GLU55 |
| C | THR81 |
| C | ALA82 |
| C | ASN117 |
| C | GLN118 |
| D | SER391 |
| D | LEU392 |
| D | ARG413 |
| 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 | MG602 |
| D | HOH722 |
| D | HOH732 |
| D | HOH807 |
| D | HOH822 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 602 |
| Chain | Residue |
| D | ASP442 |
| D | ASN469 |
| D | GLY471 |
| D | TD6601 |
| D | HOH822 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL D 603 |
| Chain | Residue |
| D | ASN470 |
| D | GLU486 |
| D | ASN494 |
| D | ASP539 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue GOL D 604 |
| Chain | Residue |
| D | GLU16 |
| D | ASN44 |
| D | SER45 |
| D | ALA46 |
| D | HOH911 |
| D | HOH964 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue FMT D 605 |
| Chain | Residue |
| D | HIS509 |
| D | GLU516 |
| D | HOH769 |
| site_id | AD7 |
| Number of Residues | 29 |
| Details | binding site for residue TD6 E 601 |
| Chain | Residue |
| E | SER391 |
| E | LEU392 |
| E | ARG413 |
| E | SER416 |
| E | GLY417 |
| E | ILE418 |
| E | ASP419 |
| E | GLY441 |
| E | ASP442 |
| E | LEU443 |
| E | SER444 |
| E | ASN469 |
| E | GLY471 |
| E | GLY472 |
| E | GLN473 |
| E | ILE474 |
| E | MG602 |
| E | HOH779 |
| E | HOH784 |
| E | HOH802 |
| E | HOH804 |
| E | HOH825 |
| E | HOH872 |
| F | PRO30 |
| F | GLU55 |
| F | THR81 |
| F | ALA82 |
| F | ASN117 |
| F | GLN118 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue MG E 602 |
| Chain | Residue |
| E | ASP442 |
| E | ASN469 |
| E | GLY471 |
| E | TD6601 |
| E | HOH784 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue FMT E 603 |
| Chain | Residue |
| E | SER288 |
| E | LEU289 |
| E | LEU295 |
| E | HOH736 |
| E | HOH855 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue FMT E 604 |
| Chain | Residue |
| E | ARG363 |
| E | GLN548 |
| site_id | AE2 |
| Number of Residues | 23 |
| Details | binding site for residue TPP F 601 |
| Chain | Residue |
| E | PRO30 |
| E | GLU55 |
| E | THR81 |
| E | ALA82 |
| F | SER391 |
| F | LEU392 |
| F | SER416 |
| F | GLY417 |
| F | ILE418 |
| F | ASP419 |
| F | GLY441 |
| F | ASP442 |
| F | LEU443 |
| F | SER444 |
| F | ASN469 |
| F | GLY471 |
| F | GLY472 |
| F | GLN473 |
| F | ILE474 |
| F | MG602 |
| F | HOH735 |
| F | HOH760 |
| F | HOH850 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue MG F 602 |
| Chain | Residue |
| F | ASP442 |
| F | ASN469 |
| F | GLY471 |
| F | TPP601 |
| F | HOH760 |
| site_id | AE4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO F 603 |
| Chain | Residue |
| F | ASP311 |
| F | HOH923 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue FMT F 604 |
| Chain | Residue |
| F | GLU505 |
| F | LEU506 |
| F | LYS507 |
| F | THR530 |
| F | HOH896 |
| site_id | AE6 |
| Number of Residues | 3 |
| Details | binding site for residue FMT F 605 |
| Chain | Residue |
| F | PRO173 |
| F | LEU174 |
| F | TYR175 |
| site_id | AE7 |
| Number of Residues | 30 |
| Details | binding site for residue TD6 G 601 |
| Chain | Residue |
| B | GLY31 |
| B | SER32 |
| B | ARG33 |
| B | GLU55 |
| B | THR78 |
| B | THR81 |
| B | ALA82 |
| B | ASN117 |
| B | GLN118 |
| G | SER391 |
| G | LEU392 |
| G | ARG413 |
| G | SER416 |
| G | GLY417 |
| G | ILE418 |
| G | ASP419 |
| G | GLY441 |
| G | ASP442 |
| G | LEU443 |
| G | SER444 |
| G | ASN469 |
| G | GLY471 |
| G | GLY472 |
| G | GLN473 |
| G | ILE474 |
| G | MG602 |
| G | HOH732 |
| G | HOH734 |
| G | HOH759 |
| G | HOH773 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue MG G 602 |
| Chain | Residue |
| G | ASP442 |
| G | ASN469 |
| G | GLY471 |
| G | TD6601 |
| G | HOH773 |
| site_id | AE9 |
| Number of Residues | 6 |
| Details | binding site for residue GOL G 603 |
| Chain | Residue |
| G | GLU16 |
| G | ASN44 |
| G | SER45 |
| G | ALA46 |
| G | HOH707 |
| G | HOH838 |
| site_id | AF1 |
| Number of Residues | 3 |
| Details | binding site for residue FMT G 604 |
| Chain | Residue |
| G | GLU209 |
| G | GLN211 |
| H | ALA203 |
| site_id | AF2 |
| Number of Residues | 27 |
| Details | binding site for residue TD6 H 601 |
| Chain | Residue |
| A | PRO30 |
| A | GLU55 |
| A | THR81 |
| A | ALA82 |
| H | ASN390 |
| H | SER391 |
| H | LEU392 |
| H | ARG413 |
| H | SER416 |
| H | GLY417 |
| H | ILE418 |
| H | ASP419 |
| H | GLY441 |
| H | ASP442 |
| H | LEU443 |
| H | SER444 |
| H | ASN469 |
| H | GLY471 |
| H | GLY472 |
| H | GLN473 |
| H | ILE474 |
| H | MG602 |
| H | HOH748 |
| H | HOH765 |
| H | HOH805 |
| H | HOH881 |
| H | HOH915 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue MG H 602 |
| Chain | Residue |
| H | ASP442 |
| H | ASN469 |
| H | GLY471 |
| H | TD6601 |
| H | HOH881 |
| 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 | HOH841 |
| H | HOH867 |
| H | HOH1022 |
| site_id | AF5 |
| Number of Residues | 4 |
| Details | binding site for residue FMT H 604 |
| Chain | Residue |
| H | ARG364 |
| H | HIS374 |
| H | ARG375 |
| H | ASP378 |
