5X8F
Ternary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with AMP and its product analogue OSB-NCoA at 1.76 angstrom
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0008756 | molecular_function | o-succinylbenzoate-CoA ligase activity |
| A | 0009234 | biological_process | menaquinone biosynthetic process |
| A | 0016405 | molecular_function | CoA-ligase activity |
| A | 0016874 | molecular_function | ligase activity |
| A | 0016878 | molecular_function | acid-thiol ligase activity |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0008756 | molecular_function | o-succinylbenzoate-CoA ligase activity |
| B | 0009234 | biological_process | menaquinone biosynthetic process |
| B | 0016405 | molecular_function | CoA-ligase activity |
| B | 0016874 | molecular_function | ligase activity |
| B | 0016878 | molecular_function | acid-thiol ligase activity |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0008756 | molecular_function | o-succinylbenzoate-CoA ligase activity |
| C | 0009234 | biological_process | menaquinone biosynthetic process |
| C | 0016405 | molecular_function | CoA-ligase activity |
| C | 0016874 | molecular_function | ligase activity |
| C | 0016878 | molecular_function | acid-thiol ligase activity |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0008756 | molecular_function | o-succinylbenzoate-CoA ligase activity |
| D | 0009234 | biological_process | menaquinone biosynthetic process |
| D | 0016405 | molecular_function | CoA-ligase activity |
| D | 0016874 | molecular_function | ligase activity |
| D | 0016878 | molecular_function | acid-thiol ligase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 43 |
| Details | binding site for residue S0N A 501 |
| Chain | Residue |
| A | LYS86 |
| A | MET242 |
| A | LEU261 |
| A | GLY263 |
| A | GLY264 |
| A | GLY287 |
| A | SER293 |
| A | GLN294 |
| A | SER389 |
| A | GLY390 |
| A | GLY391 |
| A | LEU192 |
| A | GLU392 |
| A | LYS421 |
| A | TRP422 |
| A | LYS451 |
| A | TYR452 |
| A | AMP502 |
| A | MG503 |
| A | HOH629 |
| A | HOH642 |
| A | HOH647 |
| A | PRO193 |
| A | HOH658 |
| A | HOH668 |
| A | HOH681 |
| A | HOH687 |
| A | HOH742 |
| A | HOH771 |
| A | HOH791 |
| A | HOH798 |
| A | HOH872 |
| A | HOH877 |
| A | HIS196 |
| A | HOH879 |
| D | SER220 |
| D | VAL221 |
| D | SER222 |
| A | ILE197 |
| A | SER198 |
| A | ARG218 |
| A | PHE219 |
| A | ALA238 |
| site_id | AC2 |
| Number of Residues | 23 |
| Details | binding site for residue AMP A 502 |
| Chain | Residue |
| A | THR152 |
| A | GLY265 |
| A | PRO266 |
| A | GLN284 |
| A | SER285 |
| A | TYR286 |
| A | GLY287 |
| A | MET288 |
| A | THR289 |
| A | GLU290 |
| A | ASP367 |
| A | ARG383 |
| A | LEU386 |
| A | ILE388 |
| A | ASN393 |
| A | S0N501 |
| A | HOH603 |
| A | HOH608 |
| A | HOH619 |
| A | HOH620 |
| A | HOH653 |
| A | HOH733 |
| A | HOH930 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 503 |
| Chain | Residue |
| A | PHE219 |
| A | S0N501 |
| A | HOH850 |
| A | HOH877 |
| A | HOH964 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 504 |
| Chain | Residue |
| A | GLU351 |
| A | NA512 |
| B | GLN163 |
| B | SER346 |
| B | TYR347 |
| B | ASN349 |
| B | HOH891 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 505 |
| Chain | Residue |
| A | LEU404 |
| A | HIS406 |
| A | VAL409 |
| A | HOH880 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 506 |
| Chain | Residue |
| A | MET141 |
| A | GLN142 |
| A | PHE166 |
| A | HOH706 |
| A | HOH934 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 507 |
| Chain | Residue |
| A | ASP144 |
| A | LYS345 |
| A | HOH971 |
| A | HOH1071 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 508 |
| Chain | Residue |
| A | GLY340 |
| A | VAL343 |
| A | HOH981 |
| A | HOH1000 |
| A | HOH1051 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 509 |
| Chain | Residue |
| A | HOH906 |
| A | SER153 |
| A | TYR395 |
| A | HOH653 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue MG A 510 |
| Chain | Residue |
| A | THR28 |
| A | GLU33 |
| A | HOH984 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue NA A 511 |
| Chain | Residue |
| A | ALA412 |
| A | HOH641 |
| A | HOH890 |
| A | HOH926 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue NA A 512 |
| Chain | Residue |
| A | GLU351 |
| A | MG504 |
| A | HOH845 |
| B | ASN349 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 513 |
| Chain | Residue |
| A | GLN61 |
| A | SER109 |
| A | HOH622 |
| A | HOH665 |
| A | HOH962 |
| D | ARG230 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue NA A 514 |
| Chain | Residue |
| A | GLU355 |
| A | PHE358 |
| A | HOH838 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue NA A 515 |
| Chain | Residue |
| A | MET10 |
| A | GLN14 |
| A | PEG516 |
| A | HOH1090 |
| C | HOH988 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue PEG A 516 |
| Chain | Residue |
| A | GLN14 |
| A | PHE35 |
| A | NA515 |
| A | HOH882 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue PEG A 517 |
| Chain | Residue |
| A | GLY366 |
| A | HOH806 |
| A | HOH908 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue CA A 518 |
| Chain | Residue |
| A | HIS169 |
| A | ILE197 |
| A | SER201 |
| A | CYS292 |
| A | HOH761 |
| site_id | AE1 |
| Number of Residues | 41 |
| Details | binding site for residue S0N B 501 |
| Chain | Residue |
| B | LYS86 |
| B | LEU192 |
| B | PRO193 |
| B | HIS196 |
| B | ILE197 |
| B | SER198 |
| B | PHE219 |
| B | ALA238 |
| B | MET242 |
| B | LEU261 |
| B | GLY263 |
| B | GLY264 |
| B | GLY287 |
| B | SER293 |
| B | GLN294 |
| B | SER389 |
| B | GLY390 |
| B | GLY391 |
| B | GLU392 |
| B | LYS421 |
| B | TRP422 |
| B | LYS451 |
| B | TYR452 |
| B | MG502 |
| B | HOH605 |
| B | HOH619 |
| B | HOH622 |
| B | HOH629 |
| B | HOH634 |
| B | HOH649 |
| B | HOH659 |
| B | HOH700 |
| B | HOH705 |
| B | HOH736 |
| B | HOH761 |
| B | HOH764 |
| B | HOH828 |
| B | HOH896 |
| C | SER220 |
| C | VAL221 |
| C | SER222 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 502 |
| Chain | Residue |
| B | PHE219 |
| B | S0N501 |
| B | HOH941 |
| B | HOH954 |
| B | HOH958 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 503 |
| Chain | Residue |
| B | ASN179 |
| B | PHE283 |
| B | THR297 |
| B | LEU298 |
| B | SER299 |
| B | HOH639 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue MG B 504 |
| Chain | Residue |
| B | HIS71 |
| B | LEU203 |
| B | HOH721 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 505 |
| Chain | Residue |
| B | GLU318 |
| D | MET10 |
| D | HOH738 |
| D | HOH789 |
| D | HOH933 |
| site_id | AE6 |
| Number of Residues | 1 |
| Details | binding site for residue MG B 507 |
| Chain | Residue |
| B | GLU116 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue MG B 508 |
| Chain | Residue |
| B | GLU398 |
| B | HOH665 |
| B | HOH766 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue MG B 509 |
| Chain | Residue |
| B | GLU25 |
| B | LEU215 |
| B | HOH785 |
| B | HOH837 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue NA B 510 |
| Chain | Residue |
| B | GLY340 |
| B | VAL343 |
| B | PEG520 |
| B | HOH976 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue NA B 511 |
| Chain | Residue |
| B | SER153 |
| B | GLU290 |
| B | THR365 |
| B | HOH906 |
| B | HOH922 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue NA B 512 |
| Chain | Residue |
| B | GLU351 |
| B | SER352 |
| B | HOH878 |
| B | HOH1023 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue NA B 513 |
| Chain | Residue |
| B | LYS52 |
| B | LEU76 |
| B | GLU138 |
| B | HOH613 |
| site_id | AF4 |
| Number of Residues | 2 |
| Details | binding site for residue NA B 514 |
| Chain | Residue |
| B | ARG40 |
| B | HOH710 |
| site_id | AF5 |
| Number of Residues | 3 |
| Details | binding site for residue NA B 515 |
| Chain | Residue |
| B | SER384 |
| B | VAL414 |
| B | SER415 |
| site_id | AF6 |
| Number of Residues | 3 |
| Details | binding site for residue NA B 516 |
| Chain | Residue |
| B | GLU4 |
| B | HOH889 |
| D | PRO341 |
| site_id | AF7 |
| Number of Residues | 2 |
| Details | binding site for residue NA B 517 |
| Chain | Residue |
| B | THR241 |
| B | SER245 |
| site_id | AF8 |
| Number of Residues | 8 |
| Details | binding site for residue PEG B 519 |
| Chain | Residue |
| B | THR183 |
| B | GLU184 |
| B | TYR209 |
| B | HOH683 |
| D | LEU178 |
| D | ASN179 |
| D | LEU180 |
| D | GLY181 |
| site_id | AF9 |
| Number of Residues | 8 |
| Details | binding site for residue PEG B 520 |
| Chain | Residue |
| B | ASP144 |
| B | THR165 |
| B | ASN168 |
| B | VAL343 |
| B | MET344 |
| B | LYS345 |
| B | NA510 |
| B | HOH638 |
| site_id | AG1 |
| Number of Residues | 2 |
| Details | binding site for residue CA B 521 |
| Chain | Residue |
| B | GLU25 |
| C | GLU25 |
| site_id | AG2 |
| Number of Residues | 35 |
| Details | binding site for residue S0N C 501 |
| Chain | Residue |
| C | LYS86 |
| C | PRO193 |
| C | HIS196 |
| C | ILE197 |
| C | SER198 |
| C | PHE219 |
| C | ALA238 |
| C | MET242 |
| C | LEU261 |
| C | GLY263 |
| C | GLY264 |
| C | GLY287 |
| C | SER293 |
| C | GLN294 |
| C | SER389 |
| C | GLY390 |
| C | GLY391 |
| C | GLU392 |
| C | LYS421 |
| C | TRP422 |
| C | LYS451 |
| C | TYR452 |
| C | AMP502 |
| C | MG503 |
| C | MG505 |
| C | HOH621 |
| C | HOH679 |
| C | HOH685 |
| C | HOH691 |
| C | HOH693 |
| C | HOH699 |
| C | HOH773 |
| C | HOH800 |
| C | HOH889 |
| C | HOH900 |
| site_id | AG3 |
| Number of Residues | 22 |
| Details | binding site for residue AMP C 502 |
| Chain | Residue |
| C | THR152 |
| C | GLY265 |
| C | PRO266 |
| C | GLN284 |
| C | SER285 |
| C | TYR286 |
| C | GLY287 |
| C | MET288 |
| C | THR289 |
| C | GLU290 |
| C | ASP367 |
| C | VAL379 |
| C | LEU386 |
| C | ILE388 |
| C | ASN393 |
| C | S0N501 |
| C | HOH620 |
| C | HOH637 |
| C | HOH686 |
| C | HOH728 |
| C | HOH797 |
| C | HOH844 |
| site_id | AG4 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 503 |
| Chain | Residue |
| B | HOH659 |
| B | HOH761 |
| C | PHE219 |
| C | S0N501 |
| C | HOH880 |
| site_id | AG5 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 505 |
| Chain | Residue |
| C | HIS196 |
| C | ILE197 |
| C | THR289 |
| C | S0N501 |
| C | HOH970 |
| site_id | AG6 |
| Number of Residues | 4 |
| Details | binding site for residue MG C 506 |
| Chain | Residue |
| C | LEU404 |
| C | HIS406 |
| C | VAL409 |
| C | HOH972 |
| site_id | AG7 |
| Number of Residues | 4 |
| Details | binding site for residue NA C 507 |
| Chain | Residue |
| C | TYR331 |
| C | HIS333 |
| C | TYR370 |
| C | HOH1014 |
| site_id | AG8 |
| Number of Residues | 4 |
| Details | binding site for residue NA C 508 |
| Chain | Residue |
| C | GLU33 |
| C | HOH613 |
| C | HOH781 |
| C | HOH932 |
| site_id | AG9 |
| Number of Residues | 2 |
| Details | binding site for residue NA C 509 |
| Chain | Residue |
| C | LEU76 |
| C | GLU138 |
| site_id | AH1 |
| Number of Residues | 2 |
| Details | binding site for residue NA C 510 |
| Chain | Residue |
| C | GLU335 |
| C | HOH1108 |
| site_id | AH2 |
| Number of Residues | 2 |
| Details | binding site for residue NA C 511 |
| Chain | Residue |
| A | HOH1047 |
| C | PRO330 |
| site_id | AH3 |
| Number of Residues | 3 |
| Details | binding site for residue NA C 513 |
| Chain | Residue |
| C | ASN229 |
| C | GLU232 |
| C | HOH625 |
| site_id | AH4 |
| Number of Residues | 4 |
| Details | binding site for residue NA C 514 |
| Chain | Residue |
| C | GLY423 |
| C | LYS424 |
| C | HOH870 |
| C | HOH965 |
| site_id | AH5 |
| Number of Residues | 6 |
| Details | binding site for residue PEG C 515 |
| Chain | Residue |
| A | GLU374 |
| A | HOH602 |
| C | ALA13 |
| C | GLN14 |
| C | PEG516 |
| C | HOH883 |
| site_id | AH6 |
| Number of Residues | 4 |
| Details | binding site for residue PEG C 516 |
| Chain | Residue |
| C | GLN14 |
| C | PHE35 |
| C | PEG515 |
| C | HOH612 |
| site_id | AH7 |
| Number of Residues | 5 |
| Details | binding site for residue CA C 517 |
| Chain | Residue |
| A | PRO6 |
| C | SER316 |
| C | GLU318 |
| C | GLY340 |
| C | HOH891 |
| site_id | AH8 |
| Number of Residues | 32 |
| Details | binding site for residue S0N D 501 |
| Chain | Residue |
| D | LYS86 |
| D | LEU192 |
| D | PRO193 |
| D | HIS196 |
| D | ILE197 |
| D | SER198 |
| D | PHE219 |
| D | ALA238 |
| D | MET242 |
| D | LEU261 |
| D | GLY263 |
| D | GLY264 |
| D | GLY287 |
| D | SER293 |
| D | GLN294 |
| D | SER389 |
| D | GLY390 |
| D | GLY391 |
| D | GLU392 |
| D | LYS421 |
| D | TRP422 |
| D | LYS451 |
| D | TYR452 |
| D | MG502 |
| D | HOH642 |
| D | HOH646 |
| D | HOH690 |
| D | HOH721 |
| D | HOH727 |
| D | HOH732 |
| D | HOH875 |
| D | HOH913 |
| site_id | AH9 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 502 |
| Chain | Residue |
| A | HOH642 |
| A | HOH798 |
| D | PHE219 |
| D | S0N501 |
| D | HOH881 |
| site_id | AI1 |
| Number of Residues | 7 |
| Details | binding site for residue MG D 503 |
| Chain | Residue |
| D | VAL239 |
| D | GLN240 |
| D | THR241 |
| D | GLY390 |
| D | GLY391 |
| D | HOH695 |
| D | HOH936 |
| site_id | AI2 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 504 |
| Chain | Residue |
| A | GLU25 |
| A | HOH907 |
| D | GLU25 |
| D | HOH865 |
| site_id | AI3 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 505 |
| Chain | Residue |
| D | SER172 |
| D | THR291 |
| D | CYS292 |
| D | SER293 |
| D | GLN294 |
| D | ASN342 |
| site_id | AI4 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 506 |
| Chain | Residue |
| C | HOH618 |
| D | GLU133 |
| D | HOH950 |
| D | HOH997 |
| D | HOH1010 |
| site_id | AI5 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 507 |
| Chain | Residue |
| B | HOH1035 |
| D | ILE319 |
| D | HOH786 |
| D | HOH899 |
| D | HOH942 |
| site_id | AI6 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 508 |
| Chain | Residue |
| D | GLU392 |
| D | ASN393 |
| D | TYR452 |
| D | HOH1002 |
| site_id | AI7 |
| Number of Residues | 2 |
| Details | binding site for residue NA D 509 |
| Chain | Residue |
| D | HOH725 |
| D | HOH863 |
| site_id | AI8 |
| Number of Residues | 4 |
| Details | binding site for residue NA D 510 |
| Chain | Residue |
| B | HOH658 |
| D | THR183 |
| D | GLU184 |
| D | PEG520 |
| site_id | AI9 |
| Number of Residues | 1 |
| Details | binding site for residue NA D 511 |
| Chain | Residue |
| D | ARG258 |
| site_id | AJ1 |
| Number of Residues | 4 |
| Details | binding site for residue NA D 513 |
| Chain | Residue |
| D | THR89 |
| D | HIS90 |
| D | GLU447 |
| D | HOH898 |
| site_id | AJ2 |
| Number of Residues | 2 |
| Details | binding site for residue NA D 514 |
| Chain | Residue |
| D | LYS451 |
| D | ARG454 |
| site_id | AJ3 |
| Number of Residues | 4 |
| Details | binding site for residue NA D 515 |
| Chain | Residue |
| D | GLY264 |
| D | GLY391 |
| D | ASN393 |
| D | HOH913 |
| site_id | AJ4 |
| Number of Residues | 3 |
| Details | binding site for residue NA D 516 |
| Chain | Residue |
| C | ASN470 |
| D | GLU97 |
| D | HOH945 |
| site_id | AJ5 |
| Number of Residues | 1 |
| Details | binding site for residue NA D 517 |
| Chain | Residue |
| D | HOH1051 |
| site_id | AJ6 |
| Number of Residues | 3 |
| Details | binding site for residue NA D 518 |
| Chain | Residue |
| D | GLU355 |
| D | PHE358 |
| D | HOH630 |
| site_id | AJ7 |
| Number of Residues | 4 |
| Details | binding site for residue NA D 519 |
| Chain | Residue |
| D | LEU404 |
| D | HIS406 |
| D | VAL409 |
| D | HOH917 |
| site_id | AJ8 |
| Number of Residues | 7 |
| Details | binding site for residue PEG D 520 |
| Chain | Residue |
| B | ASN179 |
| B | LEU180 |
| B | GLY181 |
| B | ARG258 |
| D | THR183 |
| D | GLU184 |
| D | NA510 |
Functional Information from PROSITE/UniProt
| site_id | PS00455 |
| Number of Residues | 12 |
| Details | AMP_BINDING Putative AMP-binding domain signature. LMYTSGTTGkPK |
| Chain | Residue | Details |
| A | LEU149-LYS160 |
