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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA S (MST1) IN COMPLEX WITH THE CANONICAL TRNATHR AND THREONYL S ADENYLATE
Keywords AMINOACYL-TRNA SYNTHETASE, THRRS, MST1, TRNA, RIBONUCLEOPROT COMPLEX, LIGASE-RNA COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   4YYE     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   THREONINE--TRNA LIGASE, MITOCHONDRIAL  A 418 3378 0
2  Protein   THREONINE--TRNA LIGASE, MITOCHONDRIAL  B 417 3366 0
3  RNA    C 74 1554 0
4  RNA    D 74 1555 0
5  Ligand   THREONINE--TRNA LIGASE, MITOCHONDRIAL  A 5 0 46
6  Ligand   THREONINE--TRNA LIGASE, MITOCHONDRIAL  B 3 0 36
7 Water     636 0 636
total       1627 9853 718
Proteins
Unit 1 ALA36 THR37 MET38 THR39 SER40 MET41 VAL42 SER43 GLN44 ARG45 GLN46 ASP47 LEU48 PHE49 MET50 THR51 ASP52 PRO53 LEU54 SER55 PRO56 GLY57 SER58 MET59 PHE60 PHE61 LEU62 PRO63 ASN64 GLY65 ALA66 LYS67 ILE68 PHE69 ASN70 LYS71 LEU72 ILE73 GLU74 PHE75 MET76 LYS77 LEU78 GLN79 GLN80 LYS81 PHE82 LYS83 PHE84 GLY85 PHE86 ASN87 GLU88 VAL89 VAL90 THR91 PRO92 LEU93 ILE94 TYR95 LYS96 LYS97 THR98 LEU99 TRP100 GLU101 LYS102 SER103 GLY104 HIS105 TRP106 GLU107 ASN108 TYR109 ALA110 ASP111 ASP112 MET113 PHE114 LYS115 VAL116 GLU117 THR118 THR119 ASP120 GLU121 GLU122 LYS123 GLU124 GLU125 TYR126 GLY127 LEU128 LYS129 PRO130 MET131 ASN132 CYS133 PRO134 GLY135 HIS136 CYS137 LEU138 ILE139 PHE140 GLY141 LYS142 LYS143 ASP144 ARG145 SER146 TYR147 ASN148 GLU149 LEU150 PRO151 LEU152 ARG153 PHE154 SER155 ASP156 PHE157 SER158 PRO159 LEU160 HIS161 ARG162 ASN163 GLU164 ALA165 SER166 GLY167 ALA168 LEU169 SER170 GLY171 LEU172 THR173 ARG174 LEU175 ARG176 LYS177 PHE178 HIS179 GLN180 ASP181 ASP182 GLY183 HIS184 ILE185 PHE186 CYS187 THR188 PRO189 SER190 GLN191 VAL192 LYS193 SER194 GLU195 ILE196 PHE197 ASN198 SER199 LEU200 LYS201 LEU202 ILE203 ASP204 ILE205 VAL206 TYR207 ASN208 LYS209 ILE210 PHE211 PRO212 SER222 ASN223 TYR224 PHE225 ILE226 ASN227 PHE228 SER229 THR230 ARG231 PRO232 ASP233 HIS234 PHE235 ILE236 GLY237 ASP238 LEU239 LYS240 VAL241 TRP242 ASN243 HIS244 ALA245 GLU246 GLN247 VAL248 LEU249 LYS250 GLU251 ILE252 LEU253 GLU254 GLU255 SER256 GLY257 LYS258 PRO259 TRP260 LYS261 LEU262 ASN263 PRO264 GLY265 ASP266 GLY267 ALA268 PHE269 TYR270 GLY271 PRO272 LYS273 LEU274 ASP275 ILE276 MET277 VAL278 THR279 ASP280 HIS281 LEU282 ARG283 LYS284 THR285 HIS286 GLN287 VAL288 ALA289 THR290 ILE291 GLN292 LEU293 ASP294 PHE295 GLN296 LEU297 PRO298 GLU299 ARG300 PHE301 ASP302 LEU303 LYS304 PHE305 LYS306 ASP307 GLN308 ASP309 ASN310 SER311 TYR312 LYS313 ARG314 PRO315 ILE316 MET317 ILE318 HIS319 ARG320 ALA321 THR322 PHE323 GLY324 SER325 ILE326 GLU327 ARG328 PHE329 MET330 ALA331 LEU332 LEU333 ILE334 ASP335 SER336 ASN337 GLU338 GLY339 ARG340 TRP341 PRO342 PHE343 TRP344 LEU345 ASN346 PRO347 TYR348 GLN349 ALA350 VAL351 ILE352 ILE353 PRO354 VAL355 ASN356 THR357 LYS358 ASN359 VAL360 GLN361 GLN362 LEU363 ASP364 MET365 CYS366 THR367 ALA368 LEU369 GLN370 LYS371 LYS372 LEU373 ARG374 ASN375 GLU376 LEU377 GLU378 ALA379 ASP380 ASP381 MET382 GLU383 PRO384 VAL385 PRO386 LEU387 ASN388 ASP389 TRP390 HIS391 PHE392 ASN393 VAL394 ASP395 LEU396 ASP397 ILE398 ARG399 ASN400 GLU401 PRO402 VAL403 GLY404 TYR405 ARG406 ILE407 LYS408 SER409 ALA410 ILE411 LEU412 LYS413 ASN414 TYR415 SER416 TYR417 LEU418 ILE419 ILE420 VAL421 GLY422 ASP423 GLU424 GLU425 VAL426 GLN427 LEU428 GLN429 LYS430 TYR431 ASN432 ILE433 ARG434 GLU435 ARG436 ASP437 ASN438 ARG439 LYS440 SER441 PHE442 GLU443 LYS444 LEU445 THR446 MET447 SER448 GLN449 ILE450 TRP451 GLU452 LYS453 PHE454 ILE455 GLU456 LEU457 GLU458 LYS459 ASN460 TYR461 LYS462
Unit 2 ALA36 THR37 MET38 THR39 SER40 MET41 VAL42 SER43 GLN44 ARG45 GLN46 ASP47 LEU48 PHE49 MET50 THR51 ASP52 PRO53 LEU54 SER55 PRO56 GLY57 SER58 MET59 PHE60 PHE61 LEU62 PRO63 ASN64 GLY65 ALA66 LYS67 ILE68 PHE69 ASN70 LYS71 LEU72 ILE73 GLU74 PHE75 MET76 LYS77 LEU78 GLN79 GLN80 LYS81 PHE82 LYS83 PHE84 GLY85 PHE86 ASN87 GLU88 VAL89 VAL90 THR91 PRO92 LEU93 ILE94 TYR95 LYS96 LYS97 THR98 LEU99 TRP100 GLU101 LYS102 SER103 GLY104 HIS105 TRP106 GLU107 ASN108 TYR109 ALA110 ASP111 ASP112 MET113 PHE114 LYS115 VAL116 GLU117 THR118 THR119 ASP120 GLU121 GLU122 LYS123 GLU124 GLU125 TYR126 GLY127 LEU128 LYS129 PRO130 MET131 ASN132 CYS133 PRO134 GLY135 HIS136 CYS137 LEU138 ILE139 PHE140 GLY141 LYS142 LYS143 ASP144 ARG145 SER146 TYR147 ASN148 GLU149 LEU150 PRO151 LEU152 ARG153 PHE154 SER155 ASP156 PHE157 SER158 PRO159 LEU160 HIS161 ARG162 ASN163 GLU164 ALA165 SER166 GLY167 ALA168 LEU169 SER170 GLY171 LEU172 THR173 ARG174 LEU175 ARG176 LYS177 PHE178 HIS179 GLN180 ASP181 ASP182 GLY183 HIS184 ILE185 PHE186 CYS187 THR188 PRO189 SER190 GLN191 VAL192 LYS193 SER194 GLU195 ILE196 PHE197 ASN198 SER199 LEU200 LYS201 LEU202 ILE203 ASP204 ILE205 VAL206 TYR207 ASN208 LYS209 ILE210 PHE211 PRO212 SER222 ASN223 TYR224 PHE225 ILE226 ASN227 PHE228 SER229 THR230 ARG231 PRO232 ASP233 HIS234 PHE235 ILE236 GLY237 ASP238 LEU239 LYS240 VAL241 TRP242 ASN243 HIS244 ALA245 GLU246 GLN247 VAL248 LEU249 LYS250 GLU251 ILE252 LEU253 GLU254 GLU255 SER256 GLY257 LYS258 PRO259 TRP260 LYS261 LEU262 ASN263 PRO264 GLY265 ASP266 GLY267 ALA268 PHE269 TYR270 GLY271 PRO272 LYS273 LEU274 ASP275 ILE276 MET277 VAL278 THR279 ASP280 HIS281 LEU282 ARG283 LYS284 THR285 HIS286 GLN287 VAL288 ALA289 THR290 ILE291 GLN292 LEU293 ASP294 PHE295 GLN296 LEU297 PRO298 GLU299 ARG300 PHE301 ASP302 LEU303 LYS304 PHE305 LYS306 ASP307 GLN308 ASP309 ASN310 SER311 TYR312 LYS313 ARG314 PRO315 ILE316 MET317 ILE318 HIS319 ARG320 ALA321 THR322 PHE323 GLY324 SER325 ILE326 GLU327 ARG328 PHE329 MET330 ALA331 LEU332 LEU333 ILE334 ASP335 SER336 ASN337 GLU338 GLY339 ARG340 TRP341 PRO342 PHE343 TRP344 LEU345 ASN346 PRO347 TYR348 GLN349 ALA350 VAL351 ILE352 ILE353 PRO354 VAL355 ASN356 THR357 LYS358 ASN359 VAL360 GLN361 GLN362 LEU363 ASP364 MET365 CYS366 THR367 ALA368 LEU369 GLN370 LYS371 LYS372 LEU373 ARG374 ASN375 GLU376 LEU377 GLU378 ALA379 ASP380 ASP381 MET382 GLU383 PRO384 VAL385 PRO386 LEU387 ASN388 ASP389 TRP390 HIS391 PHE392 ASN393 VAL394 ASP395 LEU396 ASP397 ILE398 ARG399 ASN400 GLU401 PRO402 VAL403 GLY404 TYR405 ARG406 ILE407 LYS408 SER409 ALA410 ILE411 LEU412 LYS413 ASN414 TYR415 SER416 TYR417 LEU418 ILE419 ILE420 VAL421 GLY422 ASP423 GLU424 GLU425 VAL426 GLN427 LEU428 GLN429 LYS430 TYR431 ASN432 ILE433 ARG434 GLU435 ARG436 ASP437 ASN438 LYS440 SER441 PHE442 GLU443 LYS444 LEU445 THR446 MET447 SER448 GLN449 ILE450 TRP451 GLU452 LYS453 PHE454 ILE455 GLU456 LEU457 GLU458 LYS459 ASN460 TYR461 LYS462
Nucleic acids
Unit 3 G1 U2 U3 A4 U5 A6 U7 U8 A9 G10 C11 U12 U13 A14 A15 U16 U17 G18 G19 U20 A21 G22 A23 G24 C25 A26 U27 U28 C29 G30 U31 U32 U33 U34 G35 U36 A37 A38 U39 C40 G41 A42 A43 A44 G45 G46 U47 U48 U49 G50 G51 G52 G53 U54 U55 C56 A57 A58 A59 U60 C61 C62 C63 U64 A65 A66 U67 A68 U69 A70 A71 C72 A73 C74
Unit 4 G1 U2 U3 A4 U5 A6 U7 U8 A9 G10 C11 U12 U13 A14 A15 U16 U17 G18 G19 U20 A21 G22 A23 G24 C25 A26 U27 U28 C29 G30 U31 U32 U33 U34 G35 U36 A37 A38 U39 C40 G41 A42 A43 A44 G45 G46 U47 U48 U49 G50 G51 G52 G53 U54 U55 C56 A57 A58 A59 U60 C61 C62 C63 U64 A65 A66 U67 A68 U69 A70 A71 C72 A73 C74
Ligands
Unit 5 ZN501 TSB502 SO4503 SO4504 SO4505
Unit 6 ZN501 TSB502 SO4503
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany