5Z2R
ThDP-Mn2+ complex of R395K 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 | 28 |
| Details | binding site for residue TD6 A 601 |
| Chain | Residue |
| A | SER391 |
| A | LEU443 |
| A | SER444 |
| A | TYR447 |
| A | ASN469 |
| A | GLY471 |
| A | GLY472 |
| A | GLN473 |
| A | ILE474 |
| A | MG602 |
| A | HOH717 |
| A | LEU392 |
| A | HOH747 |
| A | HOH788 |
| B | PRO30 |
| B | GLU55 |
| B | THR81 |
| B | ALA82 |
| B | ASN117 |
| B | GLN118 |
| B | FMT603 |
| A | ARG413 |
| A | SER416 |
| A | GLY417 |
| A | ILE418 |
| A | ASP419 |
| A | GLY441 |
| A | ASP442 |
| 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 | HOH747 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue FMT A 603 |
| Chain | Residue |
| A | ARG212 |
| A | ASP213 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue FMT A 604 |
| Chain | Residue |
| A | GLY31 |
| A | SER32 |
| A | ARG33 |
| A | THR78 |
| A | GLN118 |
| A | HOH724 |
| B | TD6601 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 605 |
| Chain | Residue |
| A | HIS49 |
| A | HIS50 |
| A | THR51 |
| A | ARG430 |
| A | GLN457 |
| A | HOH713 |
| B | HOH765 |
| site_id | AC6 |
| Number of Residues | 32 |
| Details | binding site for residue TD6 B 601 |
| Chain | Residue |
| A | PRO30 |
| A | GLU55 |
| A | THR81 |
| A | ALA82 |
| A | FMT604 |
| B | ASN390 |
| B | SER391 |
| B | LEU392 |
| B | ARG413 |
| 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 | PHE475 |
| B | MG602 |
| B | HOH709 |
| B | HOH717 |
| B | HOH724 |
| B | HOH824 |
| B | HOH830 |
| B | HOH915 |
| B | HOH920 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 602 |
| Chain | Residue |
| B | ASP442 |
| B | ASN469 |
| B | GLY471 |
| B | TD6601 |
| B | HOH724 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | binding site for residue FMT B 603 |
| Chain | Residue |
| A | TD6601 |
| B | GLY31 |
| B | SER32 |
| B | ARG33 |
| B | THR78 |
| B | ARG107 |
| B | GLN118 |
| B | HOH854 |
| site_id | AC9 |
| Number of Residues | 31 |
| Details | binding site for residue TD6 C 601 |
| Chain | Residue |
| 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 | PHE475 |
| C | MG602 |
| C | HOH2811 |
| C | HOH2955 |
| C | HOH2991 |
| D | PRO30 |
| D | GLU55 |
| D | THR81 |
| D | ALA82 |
| D | ASN117 |
| D | GLN118 |
| D | FMT603 |
| D | HOH711 |
| D | HOH858 |
| C | SER391 |
| C | LEU392 |
| C | ARG413 |
| C | SER416 |
| C | GLY417 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 602 |
| Chain | Residue |
| C | ASP442 |
| C | ASN469 |
| C | GLY471 |
| C | TD6601 |
| C | HOH2955 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue FMT C 603 |
| Chain | Residue |
| C | HIS49 |
| D | ARG487 |
| site_id | AD3 |
| Number of Residues | 2 |
| Details | binding site for residue FMT C 604 |
| Chain | Residue |
| C | GLN186 |
| C | HOH2813 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue FMT C 605 |
| Chain | Residue |
| C | ARG364 |
| C | ARG375 |
| C | ASP378 |
| C | HOH2887 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue FMT C 606 |
| Chain | Residue |
| C | ARG510 |
| C | PRO511 |
| C | GLN512 |
| C | GLU534 |
| C | VAL536 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue FMT C 607 |
| Chain | Residue |
| C | THR51 |
| C | ARG430 |
| C | HOH2881 |
| C | HOH2944 |
| site_id | AD7 |
| Number of Residues | 25 |
| Details | binding site for residue TD6 D 601 |
| Chain | Residue |
| C | PRO30 |
| 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 | ASN469 |
| D | GLY471 |
| D | GLY472 |
| D | GLN473 |
| D | ILE474 |
| D | MG602 |
| D | HOH750 |
| D | HOH891 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 602 |
| Chain | Residue |
| D | ASP442 |
| D | ASN469 |
| D | GLY471 |
| D | TD6601 |
| D | HOH750 |
| site_id | AD9 |
| Number of Residues | 9 |
| Details | binding site for residue FMT D 603 |
| Chain | Residue |
| C | TD6601 |
| D | GLY31 |
| D | SER32 |
| D | ARG33 |
| D | THR78 |
| D | ARG107 |
| D | GLN118 |
| D | HOH711 |
| D | HOH897 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue FMT D 604 |
| Chain | Residue |
| D | ASP213 |
| D | PHE216 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue FMT D 605 |
| Chain | Residue |
| D | GLN186 |
| D | HOH716 |
| D | HOH902 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue FMT D 606 |
| Chain | Residue |
| D | GLU505 |
| D | LEU506 |
| D | LYS507 |
| D | THR529 |
| D | THR530 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue FMT D 607 |
| Chain | Residue |
| D | THR51 |
| D | ARG430 |
| D | HOH976 |
| site_id | AE5 |
| Number of Residues | 7 |
| Details | binding site for residue FMT D 608 |
| Chain | Residue |
| D | GLU16 |
| D | ARG20 |
| D | TRP193 |
| D | GLN194 |
| D | ASP195 |
| D | HOH898 |
| D | HOH970 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue MG E 601 |
| Chain | Residue |
| E | ASP442 |
| E | ASN469 |
| E | GLY471 |
| E | TPP607 |
| E | HOH732 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue FMT E 602 |
| Chain | Residue |
| E | HIS49 |
| E | HOH850 |
| F | ARG487 |
| site_id | AE8 |
| Number of Residues | 6 |
| Details | binding site for residue FMT E 603 |
| Chain | Residue |
| E | ALA127 |
| E | SER128 |
| E | HIS129 |
| F | ARG121 |
| F | PRO123 |
| F | HOH860 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue FMT E 604 |
| Chain | Residue |
| E | ARG9 |
| E | ALA12 |
| E | GLN186 |
| E | FMT606 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue FMT E 605 |
| Chain | Residue |
| E | ARG121 |
| F | GLY94 |
| F | SER128 |
| F | HIS129 |
| F | HOH879 |
| site_id | AF2 |
| Number of Residues | 2 |
| Details | binding site for residue FMT E 606 |
| Chain | Residue |
| E | GLN186 |
| E | FMT604 |
| site_id | AF3 |
| Number of Residues | 24 |
| Details | binding site for residue TPP E 607 |
| 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 | MG601 |
| E | HOH732 |
| E | HOH757 |
| F | PRO30 |
| F | GLU55 |
| F | THR81 |
| F | ALA82 |
| F | FMT606 |
| site_id | AF4 |
| Number of Residues | 5 |
| Details | binding site for residue GOL E 608 |
| Chain | Residue |
| E | GLN141 |
| E | PRO144 |
| E | TRP185 |
| E | ARG188 |
| E | HOH726 |
| site_id | AF5 |
| Number of Residues | 29 |
| Details | binding site for residue TD6 F 601 |
| Chain | Residue |
| E | PRO30 |
| E | GLU55 |
| E | THR81 |
| E | ASN117 |
| E | GLN118 |
| E | HOH911 |
| F | SER391 |
| F | LEU392 |
| F | ARG413 |
| 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 | MG602 |
| F | HOH705 |
| F | HOH727 |
| F | HOH832 |
| F | HOH839 |
| F | HOH845 |
| site_id | AF6 |
| Number of Residues | 5 |
| Details | binding site for residue MG F 602 |
| Chain | Residue |
| F | ASP442 |
| F | ASN469 |
| F | GLY471 |
| F | TD6601 |
| F | HOH727 |
| site_id | AF7 |
| Number of Residues | 8 |
| Details | binding site for residue FMT F 603 |
| Chain | Residue |
| E | MET503 |
| E | HOH935 |
| F | HIS496 |
| F | PHE497 |
| F | GLU498 |
| F | HIS499 |
| F | ALA500 |
| F | HOH940 |
| site_id | AF8 |
| Number of Residues | 5 |
| Details | binding site for residue FMT F 604 |
| Chain | Residue |
| F | LEU267 |
| F | ARG293 |
| F | GLN296 |
| F | TRP297 |
| F | HOH837 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue FMT F 605 |
| Chain | Residue |
| E | LYS341 |
| E | ARG342 |
| F | GLN515 |
| F | GLU518 |
| F | THR519 |
| site_id | AG1 |
| Number of Residues | 7 |
| Details | binding site for residue FMT F 606 |
| Chain | Residue |
| E | TPP607 |
| F | GLY31 |
| F | SER32 |
| F | ARG33 |
| F | THR78 |
| F | ARG107 |
| F | GLN118 |
| site_id | AG2 |
| Number of Residues | 33 |
| Details | binding site for residue TD6 G 601 |
| Chain | Residue |
| G | ASN390 |
| G | SER391 |
| G | LEU392 |
| G | ARG413 |
| 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 | HOH709 |
| G | HOH723 |
| G | HOH805 |
| G | HOH829 |
| G | HOH869 |
| G | HOH884 |
| G | HOH928 |
| H | PRO30 |
| H | GLU55 |
| H | THR81 |
| H | ALA82 |
| H | GLN118 |
| H | HOH885 |
| site_id | AG3 |
| Number of Residues | 5 |
| Details | binding site for residue MN G 602 |
| Chain | Residue |
| G | ASP442 |
| G | ASN469 |
| G | GLY471 |
| G | TD6601 |
| G | HOH805 |
| site_id | AG4 |
| Number of Residues | 5 |
| Details | binding site for residue FMT G 603 |
| Chain | Residue |
| G | LEU289 |
| G | THR290 |
| G | LEU295 |
| G | ARG413 |
| H | ASN117 |
| site_id | AG5 |
| Number of Residues | 6 |
| Details | binding site for residue FMT G 604 |
| Chain | Residue |
| G | SER32 |
| G | ARG33 |
| G | THR78 |
| G | ARG107 |
| G | GLN118 |
| H | TD6601 |
| site_id | AG6 |
| Number of Residues | 5 |
| Details | binding site for residue FMT G 605 |
| Chain | Residue |
| G | ARG364 |
| G | HIS374 |
| G | ARG375 |
| G | ASP378 |
| G | HOH896 |
| site_id | AG7 |
| Number of Residues | 7 |
| Details | binding site for residue FMT G 606 |
| Chain | Residue |
| G | GLU498 |
| G | ALA501 |
| G | ALA502 |
| G | LEU506 |
| G | TYR508 |
| G | HOH740 |
| G | HOH932 |
| site_id | AG8 |
| Number of Residues | 28 |
| Details | binding site for residue TD6 H 601 |
| Chain | Residue |
| G | PRO30 |
| G | GLU55 |
| G | THR81 |
| G | ASN117 |
| G | GLN118 |
| G | FMT604 |
| G | HOH877 |
| H | SER391 |
| H | LEU392 |
| H | ARG413 |
| 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 | MG602 |
| H | HOH750 |
| H | HOH803 |
| H | HOH856 |
| site_id | AG9 |
| Number of Residues | 5 |
| Details | binding site for residue MG H 602 |
| Chain | Residue |
| H | ASP442 |
| H | ASN469 |
| H | GLY471 |
| H | TD6601 |
| H | HOH848 |
| site_id | AH1 |
| Number of Residues | 7 |
| Details | binding site for residue FMT H 603 |
| Chain | Residue |
| E | ARG138 |
| E | THR140 |
| H | ARG138 |
| H | THR140 |
| H | HOH760 |
| H | HOH761 |
| H | HOH816 |
