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 | 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 | 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 |