3HWW
Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate
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 |
| 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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE AKG A 557 |
| Chain | Residue |
| A | SER391 |
| A | HOH660 |
| A | HOH738 |
| A | LEU392 |
| A | GLY441 |
| A | ASP442 |
| A | LEU443 |
| A | SER444 |
| A | GLY471 |
| A | MG558 |
| A | NA576 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 558 |
| Chain | Residue |
| A | ASP442 |
| A | VAL467 |
| A | ASN469 |
| A | GLY471 |
| A | AKG557 |
| A | HOH738 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 559 |
| Chain | Residue |
| A | HIS21 |
| A | ASP153 |
| A | GLY157 |
| A | LEU200 |
| A | ARG201 |
| A | GLU202 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA A 560 |
| Chain | Residue |
| A | THR19 |
| A | VAL23 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 561 |
| Chain | Residue |
| A | ASP54 |
| A | ARG56 |
| A | TYR447 |
| A | ASP448 |
| A | ASN450 |
| A | NA562 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE NA A 562 |
| Chain | Residue |
| A | TYR447 |
| A | ASP448 |
| A | LEU449 |
| A | ASN450 |
| A | NA561 |
| D | ASN450 |
| D | HOH705 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL A 563 |
| Chain | Residue |
| A | ALA66 |
| A | GLN71 |
| A | LYS99 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 564 |
| Chain | Residue |
| A | SER79 |
| A | GLY80 |
| A | THR81 |
| A | ALA82 |
| D | HOH706 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA A 565 |
| Chain | Residue |
| A | SER135 |
| A | LEU136 |
| A | ASN167 |
| A | PRO169 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE NA A 566 |
| Chain | Residue |
| A | HIS132 |
| A | SER133 |
| A | HOH739 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA A 567 |
| Chain | Residue |
| A | ASP179 |
| A | ASP180 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE NA A 568 |
| Chain | Residue |
| A | ARG146 |
| A | ARG188 |
| A | GOL579 |
| site_id | BC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE NA A 569 |
| Chain | Residue |
| A | ARG212 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE NA A 570 |
| Chain | Residue |
| A | ALA203 |
| A | SER208 |
| A | GLU209 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA A 571 |
| Chain | Residue |
| A | ALA203 |
| A | SER208 |
| A | ARG325 |
| A | LEU326 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA A 572 |
| Chain | Residue |
| A | VAL252 |
| A | GLN255 |
| A | NA573 |
| A | HOH743 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 573 |
| Chain | Residue |
| A | GLN255 |
| A | LEU403 |
| A | PRO404 |
| A | TYR407 |
| A | NA572 |
| site_id | BC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 574 |
| Chain | Residue |
| A | ASP264 |
| A | GLY291 |
| A | ARG395 |
| A | ASP398 |
| A | ALA399 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 575 |
| Chain | Residue |
| A | ARG315 |
| A | LEU316 |
| A | ASP317 |
| A | ARG325 |
| A | HOH732 |
| A | HOH755 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 576 |
| Chain | Residue |
| A | ASN390 |
| A | SER391 |
| A | LEU421 |
| A | GLY441 |
| A | SER444 |
| A | AKG557 |
| site_id | CC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 577 |
| Chain | Residue |
| A | SER416 |
| A | GLY417 |
| A | ILE418 |
| D | GLU55 |
| D | ALA82 |
| D | GLN118 |
| D | HOH679 |
| site_id | CC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE NA A 578 |
| Chain | Residue |
| A | SER274 |
| site_id | CC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 579 |
| Chain | Residue |
| A | GLN141 |
| A | ASP142 |
| A | ILE143 |
| A | PRO144 |
| A | ALA145 |
| A | TRP185 |
| A | ARG188 |
| A | NA568 |
| A | HOH706 |
| site_id | CC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL A 580 |
| Chain | Residue |
| A | LYS507 |
| A | TYR508 |
| site_id | CC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE AKG D 557 |
| Chain | Residue |
| D | GLU369 |
| D | SER391 |
| D | LEU392 |
| D | VAL393 |
| D | GLY441 |
| D | ASP442 |
| D | LEU443 |
| D | VAL467 |
| D | ASN469 |
| D | MG558 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG D 558 |
| Chain | Residue |
| D | ASP442 |
| D | VAL467 |
| D | ASN469 |
| D | AKG557 |
| site_id | CC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 559 |
| Chain | Residue |
| D | TRP10 |
| D | LEU136 |
| D | PRO137 |
| D | PRO169 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE NA D 560 |
| Chain | Residue |
| D | ALA17 |
| D | ARG20 |
| D | VAL149 |
| D | ASP153 |
| D | TRP192 |
| D | PRO198 |
| D | TRP199 |
| site_id | DC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE NA D 561 |
| Chain | Residue |
| D | ALA66 |
| D | GLN71 |
| D | LYS99 |
| site_id | DC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 562 |
| Chain | Residue |
| D | ALA29 |
| D | GLU55 |
| D | VAL77 |
| D | THR78 |
| site_id | DC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE NA D 563 |
| Chain | Residue |
| D | ARG228 |
| D | SER411 |
| D | ARG413 |
| site_id | DC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 564 |
| Chain | Residue |
| D | LYS67 |
| D | TYR410 |
| D | SER411 |
| D | HOH711 |
| site_id | DC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA D 565 |
| Chain | Residue |
| D | GLY124 |
| D | MET125 |
| D | PHE126 |
| D | HIS165 |
| D | HOH714 |
| site_id | DC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 566 |
| Chain | Residue |
| A | ARG138 |
| D | ARG138 |
| D | CL568 |
| D | HOH715 |
| site_id | DC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA D 567 |
| Chain | Residue |
| A | THR140 |
| D | CL568 |
| D | HOH700 |
| D | HOH715 |
| D | HOH716 |
| site_id | DC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL D 568 |
| Chain | Residue |
| A | PRO137 |
| A | ARG138 |
| D | ARG138 |
| D | NA566 |
| D | NA567 |
| site_id | EC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL D 569 |
| Chain | Residue |
| D | HIS132 |
| D | SER133 |
| D | HIS154 |
| site_id | EC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 570 |
| Chain | Residue |
| D | SER150 |
| D | HIS320 |
| D | HIS321 |
| D | HOH729 |
| site_id | EC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL D 571 |
| Chain | Residue |
| D | GLN186 |
| D | TRP193 |
| site_id | EC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 572 |
| Chain | Residue |
| D | ILE308 |
| D | ARG324 |
| D | NA575 |
| D | HOH619 |
| site_id | EC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA D 573 |
| Chain | Residue |
| D | THR96 |
| D | GLU98 |
| site_id | EC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA D 574 |
| Chain | Residue |
| A | ARG138 |
| A | HOH719 |
| site_id | EC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA D 575 |
| Chain | Residue |
| D | ARG315 |
| D | LEU316 |
| D | ASP317 |
| D | ARG325 |
| D | NA572 |
| D | HOH729 |
| site_id | EC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA D 576 |
| Chain | Residue |
| D | LEU248 |
| D | GLY250 |
| D | GLN258 |
| D | PRO259 |
| D | LEU260 |
| D | NA577 |
| site_id | EC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 577 |
| Chain | Residue |
| D | GLY250 |
| D | LEU260 |
| D | NA576 |
| D | HOH674 |
| site_id | FC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA D 578 |
| Chain | Residue |
| D | ASP264 |
| D | LYS292 |
| site_id | FC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA D 579 |
| Chain | Residue |
| D | LYS292 |
| D | LEU295 |
| site_id | FC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA D 580 |
| Chain | Residue |
| D | GLY389 |
| D | ASN390 |
| D | SER391 |
| D | LEU421 |
| D | GLY441 |
| D | SER444 |
| site_id | FC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL D 581 |
| Chain | Residue |
| D | ASN494 |
| D | HIS496 |
| D | ARG510 |
