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 | 0044281 | biological_process | small molecule metabolic process |
| 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 | 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 |
| 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 | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0044281 | biological_process | small molecule metabolic process |
| 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 | 0044281 | biological_process | small molecule metabolic process |
| 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 |
