3HWX
Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP
Functional Information from GO Data
Chain | GOid | namespace | contents |
1 | 0000287 | molecular_function | magnesium ion binding |
1 | 0003824 | molecular_function | catalytic activity |
1 | 0009234 | biological_process | menaquinone biosynthetic process |
1 | 0016740 | molecular_function | transferase activity |
1 | 0030145 | molecular_function | manganese ion binding |
1 | 0030976 | molecular_function | thiamine pyrophosphate binding |
1 | 0042803 | molecular_function | protein homodimerization activity |
1 | 0046872 | molecular_function | metal ion binding |
1 | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
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 |
I | 0000287 | molecular_function | magnesium ion binding |
I | 0003824 | molecular_function | catalytic activity |
I | 0009234 | biological_process | menaquinone biosynthetic process |
I | 0016740 | molecular_function | transferase activity |
I | 0030145 | molecular_function | manganese ion binding |
I | 0030976 | molecular_function | thiamine pyrophosphate binding |
I | 0042803 | molecular_function | protein homodimerization activity |
I | 0046872 | molecular_function | metal ion binding |
I | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
J | 0000287 | molecular_function | magnesium ion binding |
J | 0003824 | molecular_function | catalytic activity |
J | 0009234 | biological_process | menaquinone biosynthetic process |
J | 0016740 | molecular_function | transferase activity |
J | 0030145 | molecular_function | manganese ion binding |
J | 0030976 | molecular_function | thiamine pyrophosphate binding |
J | 0042803 | molecular_function | protein homodimerization activity |
J | 0046872 | molecular_function | metal ion binding |
J | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
R | 0000287 | molecular_function | magnesium ion binding |
R | 0003824 | molecular_function | catalytic activity |
R | 0009234 | biological_process | menaquinone biosynthetic process |
R | 0016740 | molecular_function | transferase activity |
R | 0030145 | molecular_function | manganese ion binding |
R | 0030976 | molecular_function | thiamine pyrophosphate binding |
R | 0042803 | molecular_function | protein homodimerization activity |
R | 0046872 | molecular_function | metal ion binding |
R | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
S | 0000287 | molecular_function | magnesium ion binding |
S | 0003824 | molecular_function | catalytic activity |
S | 0009234 | biological_process | menaquinone biosynthetic process |
S | 0016740 | molecular_function | transferase activity |
S | 0030145 | molecular_function | manganese ion binding |
S | 0030976 | molecular_function | thiamine pyrophosphate binding |
S | 0042803 | molecular_function | protein homodimerization activity |
S | 0046872 | molecular_function | metal ion binding |
S | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
Z | 0000287 | molecular_function | magnesium ion binding |
Z | 0003824 | molecular_function | catalytic activity |
Z | 0009234 | biological_process | menaquinone biosynthetic process |
Z | 0016740 | molecular_function | transferase activity |
Z | 0030145 | molecular_function | manganese ion binding |
Z | 0030976 | molecular_function | thiamine pyrophosphate binding |
Z | 0042803 | molecular_function | protein homodimerization activity |
Z | 0046872 | molecular_function | metal ion binding |
Z | 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 | 1 |
Details | BINDING SITE FOR RESIDUE NA A 557 |
Chain | Residue |
A | GLN71 |
site_id | AC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NA A 558 |
Chain | Residue |
A | ALA203 |
site_id | AC3 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE TPP A 601 |
Chain | Residue |
A | ASP442 |
A | LEU443 |
A | SER444 |
A | ASN469 |
A | GLY471 |
A | GLY472 |
A | GLN473 |
A | ILE474 |
A | MG602 |
A | HOH659 |
A | HOH702 |
A | HOH771 |
B | PRO30 |
B | GLU55 |
B | THR81 |
B | ALA82 |
B | HOH651 |
A | SER391 |
A | LEU392 |
A | SER416 |
A | GLY417 |
A | ILE418 |
A | ASP419 |
A | GLY441 |
site_id | AC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 602 |
Chain | Residue |
A | ASP442 |
A | ASN469 |
A | GLY471 |
A | TPP601 |
A | HOH702 |
site_id | AC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA B 557 |
Chain | Residue |
B | HIS509 |
B | ARG510 |
site_id | AC6 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE TPP B 601 |
Chain | Residue |
A | PRO30 |
A | GLU55 |
A | THR81 |
A | ALA82 |
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 | MG602 |
site_id | AC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG B 602 |
Chain | Residue |
B | ASP442 |
B | ASN469 |
B | GLY471 |
B | TPP601 |
site_id | AC8 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NA I 557 |
Chain | Residue |
I | HIS49 |
site_id | AC9 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE TPP I 601 |
Chain | Residue |
I | SER391 |
I | LEU392 |
I | SER416 |
I | GLY417 |
I | ILE418 |
I | ASP419 |
I | GLY441 |
I | ASP442 |
I | LEU443 |
I | SER444 |
I | ASN469 |
I | GLY471 |
I | GLY472 |
I | GLN473 |
I | ILE474 |
I | MG602 |
J | GLU55 |
J | THR81 |
J | ALA82 |
site_id | BC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG I 602 |
Chain | Residue |
I | ASP442 |
I | ASN469 |
I | GLY471 |
I | TPP601 |
site_id | BC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL J 557 |
Chain | Residue |
J | LYS70 |
J | MET229 |
J | GLU233 |
J | ASP310 |
site_id | BC3 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE TPP J 601 |
Chain | Residue |
J | GLY471 |
J | GLY472 |
J | GLN473 |
J | ILE474 |
J | MG602 |
J | HOH723 |
I | PRO30 |
I | GLU55 |
I | ALA82 |
J | SER391 |
J | LEU392 |
J | SER416 |
J | GLY417 |
J | ILE418 |
J | ASP419 |
J | GLY441 |
J | ASP442 |
J | LEU443 |
J | SER444 |
J | ASN469 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG J 602 |
Chain | Residue |
J | ASP442 |
J | ASN469 |
J | GLY471 |
J | TPP601 |
site_id | BC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA R 557 |
Chain | Residue |
R | ARG430 |
R | GLN457 |
site_id | BC6 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NA R 558 |
Chain | Residue |
R | GLY190 |
site_id | BC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA R 559 |
Chain | Residue |
R | ASP213 |
R | PHE216 |
site_id | BC8 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE TPP R 601 |
Chain | Residue |
R | SER391 |
R | LEU392 |
R | SER416 |
R | GLY417 |
R | ILE418 |
R | ASP419 |
R | GLY441 |
R | ASP442 |
R | LEU443 |
R | SER444 |
R | ASN469 |
R | GLY471 |
R | GLY472 |
R | GLN473 |
R | ILE474 |
R | MG602 |
S | PRO30 |
S | GLU55 |
S | THR81 |
S | GLN118 |
site_id | BC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG R 602 |
Chain | Residue |
R | ASP442 |
R | ASN469 |
R | GLY471 |
R | TPP601 |
site_id | CC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA S 557 |
Chain | Residue |
S | HIS496 |
S | HIS499 |
site_id | CC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA S 559 |
Chain | Residue |
R | GLU518 |
S | GLN219 |
site_id | CC3 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE TPP S 601 |
Chain | Residue |
R | PRO30 |
R | GLU55 |
R | THR81 |
R | ALA82 |
S | SER391 |
S | LEU392 |
S | SER416 |
S | GLY417 |
S | ILE418 |
S | ASP419 |
S | GLY441 |
S | ASP442 |
S | LEU443 |
S | SER444 |
S | TYR447 |
S | ASN469 |
S | GLY471 |
S | GLY472 |
S | GLN473 |
S | ILE474 |
S | MG602 |
S | HOH805 |
site_id | CC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG S 602 |
Chain | Residue |
S | ASP442 |
S | ASN469 |
S | GLY471 |
S | TPP601 |
site_id | CC5 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE TPP Z 601 |
Chain | Residue |
1 | GLU55 |
1 | THR81 |
Z | SER391 |
Z | LEU392 |
Z | SER416 |
Z | GLY417 |
Z | ILE418 |
Z | GLY441 |
Z | ASP442 |
Z | LEU443 |
Z | SER444 |
Z | ASN469 |
Z | GLY471 |
Z | GLY472 |
Z | GLN473 |
Z | ILE474 |
Z | MG602 |
Z | HOH692 |
Z | HOH876 |
site_id | CC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG Z 602 |
Chain | Residue |
Z | ASP442 |
Z | ASN469 |
Z | GLY471 |
Z | TPP601 |
Z | HOH876 |
site_id | CC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA Z 557 |
Chain | Residue |
Z | LYS210 |
Z | ARG212 |
site_id | CC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NA Z 558 |
Chain | Residue |
Z | GLU498 |
Z | HIS499 |
site_id | CC9 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE TPP 1 601 |
Chain | Residue |
1 | SER391 |
1 | LEU392 |
1 | SER416 |
1 | GLY417 |
1 | ILE418 |
1 | ASP419 |
1 | GLY441 |
1 | ASP442 |
1 | LEU443 |
1 | SER444 |
1 | ASN469 |
1 | GLY471 |
1 | GLY472 |
1 | GLN473 |
1 | ILE474 |
1 | PHE475 |
1 | MG602 |
1 | HOH743 |
Z | PRO30 |
Z | GLU55 |
Z | THR81 |
Z | ALA82 |
Z | GLN118 |
site_id | DC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG 1 602 |
Chain | Residue |
1 | ASP442 |
1 | ASN469 |
1 | GLY471 |
1 | TPP601 |
site_id | DC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NA 1 557 |
Chain | Residue |
1 | HIS49 |
site_id | DC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL 1 558 |
Chain | Residue |
1 | LYS70 |
1 | ASP310 |