6WBD
Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000049 | molecular_function | tRNA binding |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0004812 | molecular_function | aminoacyl-tRNA ligase activity |
| A | 0004824 | molecular_function | lysine-tRNA ligase activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006412 | biological_process | translation |
| A | 0006418 | biological_process | tRNA aminoacylation for protein translation |
| A | 0006430 | biological_process | lysyl-tRNA aminoacylation |
| A | 0016874 | molecular_function | ligase activity |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000049 | molecular_function | tRNA binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003676 | molecular_function | nucleic acid binding |
| B | 0004812 | molecular_function | aminoacyl-tRNA ligase activity |
| B | 0004824 | molecular_function | lysine-tRNA ligase activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006412 | biological_process | translation |
| B | 0006418 | biological_process | tRNA aminoacylation for protein translation |
| B | 0006430 | biological_process | lysyl-tRNA aminoacylation |
| B | 0016874 | molecular_function | ligase activity |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue LYS A 601 |
| Chain | Residue |
| A | GLY215 |
| A | GLY474 |
| A | HOH712 |
| A | HOH806 |
| A | GLU239 |
| A | GLU277 |
| A | TYR279 |
| A | ASN423 |
| A | PHE425 |
| A | GLU427 |
| A | GLY472 |
| A | LEU473 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 602 |
| Chain | Residue |
| A | THR246 |
| A | GLY249 |
| A | GLU251 |
| A | ALA468 |
| A | HOH833 |
| B | ILE119 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 603 |
| Chain | Residue |
| A | PRO431 |
| A | GLU432 |
| A | GLU464 |
| B | ARG20 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 604 |
| Chain | Residue |
| A | ASP197 |
| A | PHE201 |
| A | LEU202 |
| A | GLU203 |
| A | EDO615 |
| B | SER186 |
| B | ARG190 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 605 |
| Chain | Residue |
| A | TYR285 |
| A | ASN286 |
| A | HOH780 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 606 |
| Chain | Residue |
| A | TYR241 |
| A | ARG244 |
| A | ASP458 |
| A | HOH798 |
| B | ARG166 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 607 |
| Chain | Residue |
| A | MET275 |
| A | GLU420 |
| A | LEU421 |
| A | ALA422 |
| A | ASN423 |
| A | GLY476 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 608 |
| Chain | Residue |
| A | ARG258 |
| A | HOH758 |
| A | HOH764 |
| A | HOH803 |
| B | GLU205 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 609 |
| Chain | Residue |
| A | HIS334 |
| A | THR377 |
| A | HIS380 |
| site_id | AD1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 610 |
| Chain | Residue |
| A | MET75 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 611 |
| Chain | Residue |
| A | ALA107 |
| A | SER140 |
| A | ILE141 |
| A | EDO622 |
| site_id | AD3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 612 |
| Chain | Residue |
| A | ALA191 |
| A | ASP298 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 613 |
| Chain | Residue |
| A | LEU15 |
| A | GLU18 |
| A | ARG19 |
| A | LYS22 |
| A | ASP115 |
| A | HOH889 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 614 |
| Chain | Residue |
| A | ALA180 |
| A | LYS184 |
| A | THR485 |
| A | HOH853 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 615 |
| Chain | Residue |
| A | PHE201 |
| A | EDO604 |
| A | HOH906 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 616 |
| Chain | Residue |
| A | ARG400 |
| A | ASP430 |
| A | ASP433 |
| A | HOH708 |
| A | HOH826 |
| A | HOH836 |
| B | TYR33 |
| B | HOH1272 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 617 |
| Chain | Residue |
| A | ARG268 |
| A | HIS269 |
| A | ARG479 |
| A | ILE490 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 618 |
| Chain | Residue |
| A | ASN304 |
| A | GLY306 |
| A | THR307 |
| A | GLU308 |
| site_id | AE1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 619 |
| Chain | Residue |
| A | PHE37 |
| A | GLU123 |
| A | SER140 |
| A | ILE141 |
| A | ARG142 |
| A | HOH859 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 620 |
| Chain | Residue |
| A | MET209 |
| A | TYR211 |
| A | TYR241 |
| B | PHE496 |
| B | PRO497 |
| B | HOH1243 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 621 |
| Chain | Residue |
| A | ASP433 |
| A | GLN436 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 622 |
| Chain | Residue |
| A | LEU104 |
| A | GLU139 |
| A | EDO611 |
| B | GLN29 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 623 |
| Chain | Residue |
| A | ARG324 |
| B | ARG324 |
| B | EDO1023 |
| B | EDO1024 |
| B | HOH1139 |
| B | HOH1149 |
| site_id | AE6 |
| Number of Residues | 9 |
| Details | binding site for residue EDO A 624 |
| Chain | Residue |
| A | ARG193 |
| A | GLU203 |
| A | ILE256 |
| A | EDO625 |
| A | HOH701 |
| B | ARG193 |
| B | ILE256 |
| B | EDO1010 |
| B | HOH1101 |
| site_id | AE7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 625 |
| Chain | Residue |
| A | ARG193 |
| A | ILE256 |
| A | EDO624 |
| A | HOH828 |
| B | GLU203 |
| B | GLU205 |
| B | HOH1127 |
| site_id | AE8 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 626 |
| Chain | Residue |
| A | SER186 |
| A | LYS187 |
| A | ARG190 |
| B | ASP197 |
| B | PHE201 |
| B | LEU202 |
| B | GLU203 |
| B | EDO1017 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 627 |
| Chain | Residue |
| A | GLU432 |
| B | ARG20 |
| B | LEU23 |
| B | LYS24 |
| B | ARG27 |
| site_id | AF1 |
| Number of Residues | 4 |
| Details | binding site for residue CL A 628 |
| Chain | Residue |
| A | ARG27 |
| A | ALA32 |
| A | HOH877 |
| A | HOH911 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1001 |
| Chain | Residue |
| A | ARG20 |
| A | LYS24 |
| A | ARG27 |
| B | GLU432 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1002 |
| Chain | Residue |
| B | ARG258 |
| B | LEU494 |
| B | HOH1126 |
| B | HOH1158 |
| B | HOH1175 |
| site_id | AF4 |
| Number of Residues | 10 |
| Details | binding site for residue LYS B 1003 |
| Chain | Residue |
| B | GLY215 |
| B | GLU239 |
| B | GLU277 |
| B | TYR279 |
| B | ASN423 |
| B | PHE425 |
| B | GLU427 |
| B | GLY474 |
| B | HOH1148 |
| B | HOH1220 |
| site_id | AF5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 1004 |
| Chain | Residue |
| A | ARG73 |
| A | ILE119 |
| B | THR246 |
| B | GLY249 |
| B | GLU251 |
| B | ALA468 |
| B | HOH1161 |
| site_id | AF6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1005 |
| Chain | Residue |
| A | ARG20 |
| B | PRO431 |
| B | GLU432 |
| B | ALA435 |
| B | GLU464 |
| site_id | AF7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1006 |
| Chain | Residue |
| A | ARG149 |
| B | TYR455 |
| B | ALA457 |
| B | ILE460 |
| B | GLU464 |
| site_id | AF8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1007 |
| Chain | Residue |
| B | TYR285 |
| B | ASN286 |
| B | EDO1012 |
| B | HOH1133 |
| B | HOH1147 |
| site_id | AF9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1008 |
| Chain | Residue |
| B | TYR241 |
| B | ARG244 |
| B | ASP458 |
| B | HOH1138 |
| site_id | AG1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1009 |
| Chain | Residue |
| B | GLU420 |
| B | LEU421 |
| B | ALA422 |
| B | ASN423 |
| B | GLY476 |
| site_id | AG2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1010 |
| Chain | Residue |
| A | GLU203 |
| A | EDO624 |
| A | HOH757 |
| B | ARG193 |
| B | ILE256 |
| B | HOH1258 |
| site_id | AG3 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 1011 |
| Chain | Residue |
| A | ARG346 |
| A | ASP347 |
| B | PHE85 |
| B | GLN96 |
| B | THR129 |
| B | THR131 |
| B | GLU133 |
| B | HOH1153 |
| site_id | AG4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1012 |
| Chain | Residue |
| B | TYR285 |
| B | ASN286 |
| B | ASN402 |
| B | ASP410 |
| B | EDO1007 |
| B | HOH1294 |
| site_id | AG5 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 1013 |
| Chain | Residue |
| B | MET75 |
| B | PRO152 |
| site_id | AG6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 1014 |
| Chain | Residue |
| B | ALA191 |
| B | TRP195 |
| B | HOH1152 |
| site_id | AG7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1015 |
| Chain | Residue |
| B | LYS184 |
| B | THR485 |
| B | HOH1103 |
| B | HOH1247 |
| site_id | AG8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1016 |
| Chain | Residue |
| B | PRO213 |
| B | ALA216 |
| B | ALA218 |
| B | GLU451 |
| B | ALA452 |
| B | MET453 |
| site_id | AG9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1017 |
| Chain | Residue |
| A | LYS187 |
| A | EDO626 |
| A | HOH766 |
| B | ASP197 |
| B | ASP200 |
| B | PHE201 |
| site_id | AH1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1018 |
| Chain | Residue |
| B | GLY306 |
| B | THR307 |
| B | HOH1121 |
| B | HOH1124 |
| site_id | AH2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1019 |
| Chain | Residue |
| B | ARG268 |
| B | HIS269 |
| B | ARG479 |
| B | HOH1102 |
| B | HOH1265 |
| site_id | AH3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1020 |
| Chain | Residue |
| B | PHE37 |
| B | GLU123 |
| B | SER140 |
| B | ILE141 |
| B | ARG142 |
| site_id | AH4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1021 |
| Chain | Residue |
| A | ASP347 |
| B | ARG78 |
| B | PHE85 |
| B | ALA86 |
| B | GLN87 |
| B | GLN96 |
| site_id | AH5 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 1022 |
| Chain | Residue |
| B | ASP433 |
| B | GLN436 |
| site_id | AH6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1023 |
| Chain | Residue |
| A | ARG324 |
| A | EDO623 |
| A | HOH729 |
| B | ARG324 |
| B | HOH1156 |
| site_id | AH7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1024 |
| Chain | Residue |
| A | EDO623 |
| B | ASN286 |
| B | ASP290 |
| B | ARG324 |
| B | HOH1182 |
| site_id | AH8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 1025 |
| Chain | Residue |
| B | LEU356 |
| B | ALA376 |
| site_id | AH9 |
| Number of Residues | 3 |
| Details | binding site for residue CL B 1026 |
| Chain | Residue |
| B | ARG27 |
| B | ALA32 |
| B | HOH1272 |
