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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 |