5Z2P
ThDP-Mn2+ complex of R413K 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 | MN602 |
| A | FMT608 |
| A | LEU392 |
| A | HOH722 |
| A | HOH741 |
| A | HOH899 |
| B | GLU55 |
| B | THR81 |
| B | ALA82 |
| B | GLN118 |
| B | FMT605 |
| B | HOH801 |
| A | ARG395 |
| A | SER416 |
| A | GLY417 |
| A | ILE418 |
| A | ASP419 |
| A | GLY441 |
| A | ASP442 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MN A 602 |
| Chain | Residue |
| A | ASP442 |
| A | ASN469 |
| A | GLY471 |
| A | TD6601 |
| A | HOH899 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue FMT A 603 |
| Chain | Residue |
| A | ARG364 |
| A | HIS374 |
| A | ASP378 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue FMT A 604 |
| Chain | Residue |
| A | GLN512 |
| A | ASN513 |
| A | HOH825 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue FMT A 605 |
| Chain | Residue |
| A | LYS210 |
| A | LEU336 |
| B | ILE361 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue FMT A 606 |
| Chain | Residue |
| A | ARG487 |
| B | HIS49 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue FMT A 607 |
| Chain | Residue |
| A | SER32 |
| A | ARG33 |
| A | THR78 |
| A | ARG107 |
| A | GLN118 |
| A | HOH893 |
| B | TD6601 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue FMT A 608 |
| Chain | Residue |
| A | ASN390 |
| A | SER391 |
| A | VAL394 |
| A | ARG395 |
| A | LYS413 |
| A | SER416 |
| A | TD6601 |
| site_id | AC9 |
| Number of Residues | 27 |
| Details | binding site for residue TD6 B 601 |
| Chain | Residue |
| A | PRO30 |
| A | GLU55 |
| A | THR81 |
| A | ALA82 |
| A | GLN118 |
| A | FMT607 |
| B | ASN390 |
| B | SER391 |
| B | LEU392 |
| B | ARG395 |
| B | LYS413 |
| 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 | MN602 |
| B | HOH855 |
| B | HOH864 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue MN B 602 |
| Chain | Residue |
| B | ASP442 |
| B | ASN469 |
| B | GLY471 |
| B | TD6601 |
| B | HOH838 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue FMT B 603 |
| Chain | Residue |
| B | MET1 |
| B | GLN141 |
| B | THR181 |
| B | GLY182 |
| site_id | AD3 |
| Number of Residues | 3 |
| Details | binding site for residue FMT B 604 |
| Chain | Residue |
| B | LYS70 |
| B | PRO72 |
| B | LYS99 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue FMT B 605 |
| Chain | Residue |
| B | ARG33 |
| B | THR78 |
| B | ARG107 |
| B | GLN118 |
| A | TD6601 |
| B | SER32 |
| site_id | AD5 |
| Number of Residues | 28 |
| Details | binding site for residue TD6 C 601 |
| Chain | Residue |
| C | ASN390 |
| C | SER391 |
| C | LEU392 |
| C | ARG395 |
| 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 | MN602 |
| C | HOH702 |
| C | HOH779 |
| C | HOH856 |
| C | HOH875 |
| C | HOH937 |
| D | GLU55 |
| D | THR81 |
| D | ALA82 |
| D | GLN118 |
| D | FMT603 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue MN C 602 |
| Chain | Residue |
| C | ASP442 |
| C | ASN469 |
| C | GLY471 |
| C | TD6601 |
| C | HOH856 |
| site_id | AD7 |
| Number of Residues | 7 |
| Details | binding site for residue FMT C 603 |
| Chain | Residue |
| C | GLY31 |
| C | SER32 |
| C | ARG33 |
| C | THR78 |
| C | ARG107 |
| C | GLN118 |
| D | TD6601 |
| site_id | AD8 |
| Number of Residues | 30 |
| Details | binding site for residue TD6 D 601 |
| Chain | Residue |
| C | PRO30 |
| C | GLU55 |
| C | THR81 |
| C | ALA82 |
| C | ASN117 |
| C | GLN118 |
| C | FMT603 |
| C | HOH706 |
| D | ASN390 |
| D | SER391 |
| D | LEU392 |
| D | ARG395 |
| D | LYS413 |
| 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 | HOH791 |
| D | HOH914 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue MN D 602 |
| Chain | Residue |
| D | ASP442 |
| D | ASN469 |
| D | GLY471 |
| D | TD6601 |
| D | HOH746 |
| site_id | AE1 |
| Number of Residues | 8 |
| Details | binding site for residue FMT D 603 |
| Chain | Residue |
| C | TD6601 |
| D | SER32 |
| D | ARG33 |
| D | THR78 |
| D | ARG107 |
| D | GLN118 |
| D | HOH764 |
| D | HOH822 |
| site_id | AE2 |
| Number of Residues | 11 |
| Details | binding site for residue GOL D 604 |
| Chain | Residue |
| D | GLU16 |
| D | THR19 |
| D | ARG20 |
| D | TRP193 |
| D | GLN194 |
| D | ASP195 |
| D | HOH702 |
| D | HOH912 |
| E | GLU354 |
| E | GLN358 |
| E | HOH915 |
| site_id | AE3 |
| Number of Residues | 25 |
| Details | binding site for residue TD6 E 601 |
| Chain | Residue |
| E | SER391 |
| E | LEU392 |
| E | ARG395 |
| 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 | HOH733 |
| E | HOH751 |
| E | HOH778 |
| E | HOH799 |
| G | PRO30 |
| G | GLU55 |
| G | ALA82 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue MN E 602 |
| Chain | Residue |
| E | ASP442 |
| E | ASN469 |
| E | GLY471 |
| E | TD6601 |
| E | HOH751 |
| site_id | AE5 |
| Number of Residues | 2 |
| Details | binding site for residue FMT E 603 |
| Chain | Residue |
| E | LYS236 |
| E | TRP240 |
| site_id | AE6 |
| Number of Residues | 7 |
| Details | binding site for residue FMT E 604 |
| Chain | Residue |
| E | GLU505 |
| E | LEU506 |
| E | LYS507 |
| E | THR529 |
| E | THR530 |
| E | HOH748 |
| E | HOH938 |
| site_id | AE7 |
| Number of Residues | 2 |
| Details | binding site for residue FMT E 605 |
| Chain | Residue |
| E | GLY97 |
| E | LYS99 |
| site_id | AE8 |
| Number of Residues | 28 |
| Details | binding site for residue TD6 F 601 |
| Chain | Residue |
| F | ASN390 |
| F | SER391 |
| F | LEU392 |
| F | ARG395 |
| 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 | MN602 |
| F | HOH738 |
| F | HOH767 |
| F | HOH772 |
| H | GLU55 |
| H | THR81 |
| H | ALA82 |
| H | ASN117 |
| H | GLN118 |
| H | FMT603 |
| H | HOH760 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue MN F 602 |
| Chain | Residue |
| F | ASP442 |
| F | ASN469 |
| F | GLY471 |
| F | TD6601 |
| F | HOH724 |
| site_id | AF1 |
| Number of Residues | 3 |
| Details | binding site for residue FMT F 603 |
| Chain | Residue |
| F | HIS496 |
| H | MET503 |
| H | GLU505 |
| site_id | AF2 |
| Number of Residues | 5 |
| Details | binding site for residue FMT F 604 |
| Chain | Residue |
| F | GLU498 |
| F | ALA502 |
| F | LEU506 |
| F | TYR508 |
| F | HOH926 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue FMT F 605 |
| Chain | Residue |
| F | GLN141 |
| F | GLY182 |
| F | TRP185 |
| F | FMT607 |
| F | HOH817 |
| site_id | AF4 |
| Number of Residues | 8 |
| Details | binding site for residue FMT F 606 |
| Chain | Residue |
| F | LYS67 |
| F | ARG228 |
| F | VAL409 |
| F | TYR410 |
| F | SER411 |
| F | HOH779 |
| F | HOH805 |
| F | HOH870 |
| site_id | AF5 |
| Number of Residues | 3 |
| Details | binding site for residue FMT F 607 |
| Chain | Residue |
| F | THR181 |
| F | GLY182 |
| F | FMT605 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue FMT F 608 |
| Chain | Residue |
| F | SER32 |
| F | ARG33 |
| F | THR78 |
| F | ARG107 |
| F | GLN118 |
| H | TD6601 |
| site_id | AF7 |
| Number of Residues | 24 |
| Details | binding site for residue TD6 G 601 |
| Chain | Residue |
| E | PRO30 |
| E | GLU55 |
| E | THR81 |
| E | GLN118 |
| G | ASN390 |
| G | SER391 |
| G | LEU392 |
| G | ARG395 |
| G | SER416 |
| G | GLY417 |
| G | ILE418 |
| G | GLY441 |
| G | ASP442 |
| G | LEU443 |
| G | SER444 |
| G | TYR447 |
| G | ASN469 |
| G | GLY471 |
| G | GLY472 |
| G | GLN473 |
| G | ILE474 |
| G | MN602 |
| G | HOH704 |
| G | HOH718 |
| site_id | AF8 |
| Number of Residues | 5 |
| Details | binding site for residue MN G 602 |
| Chain | Residue |
| G | ASP442 |
| G | ASN469 |
| G | GLY471 |
| G | TD6601 |
| G | HOH743 |
| site_id | AF9 |
| Number of Residues | 3 |
| Details | binding site for residue FMT G 603 |
| Chain | Residue |
| G | GLU233 |
| G | ASP311 |
| G | HOH810 |
| site_id | AG1 |
| Number of Residues | 7 |
| Details | binding site for residue FMT G 604 |
| Chain | Residue |
| E | PHE488 |
| E | TYR489 |
| G | ALA29 |
| G | PRO30 |
| G | GLY31 |
| G | SER34 |
| G | THR38 |
| site_id | AG2 |
| Number of Residues | 5 |
| Details | binding site for residue GOL G 605 |
| Chain | Residue |
| G | GLU16 |
| G | ARG20 |
| G | TRP193 |
| G | ASP195 |
| G | HOH781 |
| site_id | AG3 |
| Number of Residues | 29 |
| Details | binding site for residue TD6 H 601 |
| Chain | Residue |
| F | PRO30 |
| F | GLU55 |
| F | THR81 |
| F | ALA82 |
| F | ASN117 |
| F | GLN118 |
| F | FMT608 |
| F | HOH848 |
| H | ASN390 |
| H | SER391 |
| H | LEU392 |
| H | ARG395 |
| 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 | HOH735 |
| H | HOH780 |
| site_id | AG4 |
| Number of Residues | 5 |
| Details | binding site for residue MN H 602 |
| Chain | Residue |
| H | ASP442 |
| H | ASN469 |
| H | GLY471 |
| H | TD6601 |
| H | HOH726 |
| site_id | AG5 |
| Number of Residues | 7 |
| Details | binding site for residue FMT H 603 |
| Chain | Residue |
| F | TD6601 |
| H | SER32 |
| H | ARG33 |
| H | THR78 |
| H | ARG107 |
| H | GLN118 |
| H | HOH719 |
| site_id | AG6 |
| Number of Residues | 12 |
| Details | binding site for Di-peptide ALA C 145 and ARG C 188 |
| Chain | Residue |
| C | ILE143 |
| C | PRO144 |
| C | ARG146 |
| C | TRP147 |
| C | LEU148 |
| C | VAL149 |
| C | SER184 |
| C | TRP185 |
| C | GLN186 |
| C | GLN187 |
| C | LEU189 |
| C | GLY190 |
