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 | 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 | 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 |