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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AGROBACTERIUM RADIOBACTER K84 AGNB2 LEURS-TRNA-LEUAMS
Keywords LIGASE-RNA COMPLEX, LEUCINE-TRNA, LEUCINE-TRNA LIGASE ACTIVI L-LEUCINE + TRNA(LEU) GIVES AMP + DIPHOSPHATE + L-LEUCYL-TR AMINOACYL- TRNA EDITING ACTIVITY, AMINOACYL-TRNA SYNTHETASE PROTEIN BIOSYNTHESIS, TOXIC MOEITY 84 RESISTANCE
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   5AH5     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   LEUCINE--TRNA LIGASE  A 789 6250 0
2  Protein   LEUCINE--TRNA LIGASE  B 771 6114 0
3  RNA    C 80 1702 0
4  RNA    D 81 1721 0
5  Ligand   LEUCINE--TRNA LIGASE  A 3 0 37
6  Ligand   LEUCINE--TRNA LIGASE  B 4 0 42
7  Ligand   TRNA-LEU TAA ISOACCEPTOR  C 2 0 6
8  Ligand   TRNA-LEU TAA ISOACCEPTOR  D 2 0 6
9 Water     871 0 871
total       2603 15787 962
Proteins
Unit 1 GLN2 TYR3 ASP4 HIS5 ARG6 SER7 ARG8 ASP9 ALA10 PHE11 TRP12 GLN13 GLN14 LYS15 TRP16 ASP17 GLU18 LYS19 ARG20 ILE21 PHE22 ASP23 TRP24 ASP25 PRO26 SER27 SER28 PRO29 GLY30 LYS31 LYS32 PHE33 TYR34 VAL35 LEU36 GLU37 MET38 PHE39 PRO40 TYR41 THR42 SER43 GLY44 HIS45 LEU46 HIS47 ILE48 GLY49 HIS50 VAL51 ARG52 ASN53 TYR54 SER55 MET56 GLY57 ASP58 THR59 LEU60 ALA61 ARG62 MET63 GLN64 ILE65 ALA66 ARG67 GLY68 TYR69 SER70 VAL71 LEU72 HIS73 PRO74 MET75 GLY76 TRP77 ASP78 SER79 PHE80 GLY81 LEU82 PRO83 ALA84 GLU85 ASN86 ALA87 ALA88 ARG89 LYS90 PHE91 GLY92 THR93 HIS94 PRO95 ALA96 LYS97 PHE98 THR99 GLN100 ASP101 ALA102 ILE103 ASP104 SER105 MET106 LYS107 ARG108 SER109 MET110 MET111 GLN112 LEU113 GLY114 PHE115 GLY116 TYR117 SER118 TRP119 ALA120 ASN121 GLU122 LEU123 ALA124 THR125 CYS126 SER127 PRO128 THR129 TYR130 VAL131 LEU132 ALA133 GLN134 GLN135 LYS136 LEU137 PHE138 LEU139 ASP140 LEU141 TYR142 ARG143 LYS144 GLY145 LEU146 ILE147 TYR148 ARG149 ASP150 ASP151 THR152 TYR153 VAL154 TYR155 TRP156 ASP157 PRO158 VAL159 GLU160 GLN161 THR162 VAL163 LEU164 ALA165 ALA166 GLU167 GLN168 VAL169 ILE170 ASP171 GLY172 LYS173 GLY174 TRP175 ARG176 SER177 GLY178 ALA179 ALA180 VAL181 TYR182 LYS183 ARG184 ARG185 THR186 PRO187 GLN188 TRP189 PHE190 VAL191 ASP192 ILE193 ARG194 SER195 TYR196 ALA197 ASP198 ARG199 LEU200 LEU201 ASP202 ASP203 LEU204 GLU205 SER206 LEU207 GLU208 GLY209 TRP210 PRO211 THR212 SER213 VAL214 ARG215 ASN216 ILE217 GLN218 ARG219 ASN220 TRP221 ILE222 GLY223 ARG224 THR225 GLU226 GLY227 ALA228 GLU229 VAL230 ARG231 PHE232 LEU233 VAL234 GLU235 ALA236 SER237 ASP238 LEU239 THR240 ILE241 ASN242 ALA243 PHE244 THR245 THR246 ARG247 LEU248 ASP249 THR250 LEU251 ALA252 GLY253 CYS254 THR255 PHE256 ILE257 ALA258 LEU259 ALA260 PRO261 GLU262 HIS263 THR264 ILE265 LEU266 ASP267 GLU268 MET275 ARG276 ALA277 SER278 VAL279 LYS280 ASP281 TYR282 CYS283 GLU284 SER285 ILE286 LEU287 VAL288 LEU289 SER290 SER291 GLU292 GLU293 ARG294 SER295 ALA296 GLY297 ALA298 LYS299 SER300 GLY301 ILE302 PHE303 THR304 GLY305 LEU306 MET307 VAL308 VAL309 ASN310 PRO311 LEU312 ASN313 GLN314 GLU315 ARG316 VAL317 PRO318 LEU319 TYR320 VAL321 ALA322 ASN323 TYR324 VAL325 MET326 PRO327 ASP328 PHE329 GLY330 THR331 GLY332 ALA333 VAL334 ILE335 GLY336 VAL337 PRO338 ASP341 GLU342 ARG343 ASP344 ALA345 ASP346 PHE347 GLY348 ALA349 LEU350 PHE351 GLY352 LEU353 PRO354 VAL355 ARG356 VAL357 VAL358 SER378 HIS379 SER380 LEU381 VAL382 ASP383 GLY384 LEU385 THR386 SER387 SER388 ALA389 ALA390 ARG391 GLU392 ILE393 LEU394 ILE395 ALA396 HIS397 LEU398 SER399 GLU400 LYS401 LEU402 GLU403 GLY404 GLN405 LYS406 SER407 THR408 GLN409 TYR410 ARG411 LEU412 GLN413 ASN414 TRP415 SER416 ILE417 SER418 ARG419 GLN420 ARG421 TYR422 TRP423 GLY424 CYS425 PRO426 ILE427 PRO428 ILE429 ILE430 HIS431 CYS432 SER433 GLU434 CYS435 GLY436 THR437 ILE438 PRO439 VAL440 ALA441 GLU442 GLU443 GLN444 LEU445 PRO446 ILE447 LEU448 LEU449 PRO450 ASP451 HIS452 LEU453 ILE454 SER455 GLU456 GLY457 SER458 GLY459 SER460 PRO461 LEU462 SER463 ARG464 ASP465 GLU466 SER467 TRP468 MET469 LYS470 ALA471 LYS472 CYS473 PRO474 GLN475 CYS476 GLY477 GLY478 ASP479 ALA480 ALA481 ARG482 ASP483 PRO484 ASP485 THR486 MET487 ASP488 THR489 PHE490 VAL491 ASP492 SER493 SER494 TRP495 TYR496 PHE497 LEU498 ARG499 TYR500 PRO501 SER502 PRO503 SER504 SER505 PRO506 ASN507 PRO508 ILE509 ASP510 SER511 SER512 LEU513 CYS514 ASN515 LYS516 ILE517 ALA518 PRO519 ALA520 ASP521 VAL522 TYR523 ILE524 GLY525 GLY526 ILE527 GLU528 HIS529 ALA530 THR531 LEU532 HIS533 LEU534 ILE535 TYR536 SER537 ARG538 PHE539 ILE540 THR541 LYS542 VAL543 LEU544 HIS545 ASP546 LEU547 GLY548 TYR549 ILE550 GLU551 PHE552 ASP553 GLU554 PRO555 PHE556 VAL557 GLU558 LEU559 TYR560 ASN561 GLN562 GLY563 MET564 VAL565 ASN566 ASP567 VAL568 HIS569 GLY570 ARG571 LYS572 GLN573 SER574 LYS575 SER576 LEU577 GLY578 ASN579 VAL580 THR581 ASP582 PRO583 SER584 VAL585 VAL586 VAL587 GLN588 GLU589 PHE590 GLY591 ALA592 ASP593 ALA594 VAL595 ARG596 CYS597 TYR598 LEU599 LEU600 PHE601 LYS602 THR603 THR604 TYR605 ASN606 ALA607 PRO608 ILE609 ASN610 TRP611 GLU612 ASP613 SER614 GLY615 PRO616 GLN617 ALA618 MET619 ARG620 SER621 TYR622 LEU623 GLU624 ARG625 VAL626 CYS627 ARG628 LEU629 PHE630 THR631 ASN632 ASN633 LEU634 ASP635 ARG636 LEU637 ARG638 SER639 SER640 SER641 ALA642 ILE643 GLU644 ILE645 CYS646 PRO647 ASP648 ASP649 CYS650 GLU651 ASN652 GLU653 GLU654 ASP655 ARG656 GLU657 ILE658 ALA659 ARG660 GLN661 LEU662 GLN663 LEU664 ALA665 ILE666 GLY667 LYS668 VAL669 THR670 ALA671 ASP672 VAL673 GLU674 ARG675 PHE676 HIS677 PHE678 ASN679 ALA680 ALA681 ILE682 ALA683 ALA684 ILE685 MET686 SER687 VAL688 THR689 ASN690 LEU691 LEU692 TYR693 GLU694 LYS695 GLY696 GLY697 LYS698 ALA699 SER700 PRO701 THR702 VAL703 LEU704 ALA705 GLY706 SER707 LEU708 ARG709 LEU710 LEU711 VAL712 ARG713 LEU714 LEU715 ALA716 PRO717 PHE718 ALA719 PRO720 HIS721 ILE722 SER723 GLU724 GLU725 LEU726 TRP727 ALA728 LEU729 SER730 GLY731 CYS732 ASN733 SER734 LEU735 VAL736 ALA737 ALA738 GLU739 PRO740 TRP741 PRO742 THR743 ILE744 ASN745 GLU746 ARG747 LEU748 VAL749 GLN750 ALA751 GLU752 ASN753 ILE754 VAL755 LEU756 PRO757 VAL758 GLN759 ILE760 ASN761 GLY762 LYS763 LEU764 ILE765 ARG766 THR767 MET768 THR769 ILE770 PRO771 VAL772 ASN773 LEU774 ALA775 GLU776 GLU777 ASP778 ILE779 LEU780 SER781 THR782 VAL783 LEU784 ALA785 LEU786 PRO787 GLU788 VAL789 ARG790 SER791 ARG792 LEU793 SER794 ASP795 ARG796 ASP797 LEU798 LYS799 ASN800 TYR801 ARG802 TYR803 VAL804 PRO805 ASN806 ARG807 ILE808 ILE809 ASN810 LEU811 VAL812 VAL813 GLY814 LEU815 GLU816 HIS817
Unit 2 GLN2 TYR3 ASP4 HIS5 ARG6 SER7 ARG8 ASP9 ALA10 PHE11 TRP12 GLN13 GLN14 LYS15 TRP16 ASP17 GLU18 LYS19 ARG20 ILE21 PHE22 ASP23 TRP24 ASP25 PRO26 SER27 SER28 PRO29 GLY30 LYS31 LYS32 PHE33 TYR34 VAL35 LEU36 GLU37 MET38 PHE39 PRO40 TYR41 THR42 SER43 GLY44 HIS45 LEU46 HIS47 ILE48 GLY49 HIS50 VAL51 ARG52 ASN53 TYR54 SER55 MET56 GLY57 ASP58 THR59 LEU60 ALA61 ARG62 MET63 GLN64 ILE65 ALA66 ARG67 GLY68 TYR69 SER70 VAL71 LEU72 HIS73 PRO74 MET75 GLY76 TRP77 ASP78 SER79 PHE80 GLY81 LEU82 PRO83 ALA84 GLU85 ASN86 ALA87 ALA88 ARG89 LYS90 PHE91 GLY92 THR93 HIS94 PRO95 ALA96 LYS97 PHE98 THR99 GLN100 ASP101 ALA102 ILE103 ASP104 SER105 MET106 LYS107 ARG108 SER109 MET110 MET111 GLN112 LEU113 GLY114 PHE115 GLY116 TYR117 SER118 TRP119 ALA120 ASN121 GLU122 LEU123 ALA124 THR125 CYS126 SER127 PRO128 THR129 TYR130 VAL131 LEU132 ALA133 GLN134 GLN135 LYS136 LEU137 PHE138 LEU139 ASP140 LEU141 TYR142 ARG143 LYS144 GLY145 LEU146 ILE147 TYR148 ARG149 ASP150 ASP151 THR152 TYR153 VAL154 TYR155 TRP156 ASP157 PRO158 VAL159 GLU160 GLN161 THR162 VAL163 LEU164 ALA165 ALA166 GLU167 GLN168 VAL169 ILE170 ASP171 GLY172 LYS173 GLY174 TRP175 ARG176 SER177 GLY178 ALA179 ALA180 VAL181 TYR182 LYS183 ARG184 ARG185 THR186 PRO187 GLN188 TRP189 PHE190 VAL191 ASP192 ILE193 ARG194 SER195 TYR196 ALA197 ASP198 ARG199 LEU200 LEU201 ASP202 ASP203 LEU204 GLU205 SER206 LEU207 GLU208 GLY209 TRP210 PRO211 THR212 SER213 VAL214 ARG215 ASN216 ILE217 GLN218 ARG219 ASN220 TRP221 ILE222 GLY223 ARG224 THR225 GLU226 GLY227 ALA228 GLU229 VAL230 ARG231 PHE232 LEU233 VAL234 GLU235 ALA236 SER237 ASP238 LEU239 THR240 ILE241 ASN242 ALA243 PHE244 THR245 THR246 ARG247 LEU248 ASP249 THR250 LEU251 ALA252 GLY253 CYS254 THR255 PHE256 ILE257 ALA258 LEU259 ALA260 PRO261 GLU262 HIS263 THR264 ILE265 LEU266 ASP267 ARG276 ALA277 SER278 VAL279 LYS280 ASP281 TYR282 CYS283 GLU284 SER285 ILE286 LEU287 VAL288 LEU289 SER290 SER291 GLU292 GLU293 ARG294 SER295 ALA296 GLY297 ALA298 LYS299 SER300 GLY301 ILE302 PHE303 THR304 GLY305 LEU306 MET307 VAL308 VAL309 ASN310 PRO311 LEU312 ASN313 GLN314 GLU315 ARG316 VAL317 PRO318 LEU319 TYR320 VAL321 ALA322 ASN323 TYR324 VAL325 MET326 PRO327 ASP328 PHE329 GLY330 THR331 GLY332 ALA333 VAL334 ILE335 GLY336 VAL337 PRO338 ASP341 GLU342 ARG343 ASP344 ALA345 ASP346 PHE347 GLY348 ALA349 LEU350 THR386 SER387 SER388 ALA389 ALA390 ARG391 GLU392 ILE393 LEU394 ILE395 ALA396 HIS397 LEU398 SER399 GLU400 LYS401 LEU402 GLU403 GLY404 GLN405 LYS406 SER407 THR408 GLN409 TYR410 ARG411 LEU412 GLN413 ASN414 TRP415 SER416 ILE417 SER418 ARG419 GLN420 ARG421 TYR422 TRP423 GLY424 CYS425 PRO426 ILE427 PRO428 ILE429 ILE430 HIS431 CYS432 SER433 GLU434 CYS435 GLY436 THR437 ILE438 PRO439 VAL440 ALA441 GLU442 GLU443 GLN444 LEU445 PRO446 ILE447 LEU448 LEU449 PRO450 ASP451 HIS452 LEU453 ILE454 SER455 GLU456 GLY457 SER458 GLY459 SER460 PRO461 LEU462 SER463 ARG464 ASP465 GLU466 SER467 TRP468 MET469 LYS470 ALA471 LYS472 CYS473 PRO474 GLN475 CYS476 GLY477 GLY478 ASP479 ALA480 ALA481 ARG482 ASP483 PRO484 ASP485 THR486 MET487 ASP488 THR489 PHE490 VAL491 ASP492 SER493 SER494 TRP495 TYR496 PHE497 LEU498 ARG499 TYR500 PRO501 SER502 PRO503 SER504 SER505 PRO506 ASN507 PRO508 ILE509 ASP510 SER511 SER512 LEU513 CYS514 ASN515 LYS516 ILE517 ALA518 PRO519 ALA520 ASP521 VAL522 TYR523 ILE524 GLY525 GLY526 ILE527 GLU528 HIS529 ALA530 THR531 LEU532 HIS533 LEU534 ILE535 TYR536 SER537 ARG538 PHE539 ILE540 THR541 LYS542 VAL543 LEU544 HIS545 ASP546 LEU547 GLY548 TYR549 ILE550 GLU551 PHE552 ASP553 GLU554 PRO555 PHE556 VAL557 GLU558 LEU559 TYR560 ASN561 GLN562 GLY563 MET564 VAL565 ASN566 ASP567 VAL568 HIS569 GLY570 ARG571 LYS572 GLN573 SER574 LYS575 SER576 LEU577 GLY578 ASN579 VAL580 THR581 ASP582 PRO583 SER584 VAL585 VAL586 VAL587 GLN588 GLU589 PHE590 GLY591 ALA592 ASP593 ALA594 VAL595 ARG596 CYS597 TYR598 LEU599 LEU600 PHE601 LYS602 THR603 THR604 TYR605 ASN606 ALA607 PRO608 ILE609 ASN610 TRP611 GLU612 ASP613 SER614 GLY615 PRO616 GLN617 ALA618 MET619 ARG620 SER621 TYR622 LEU623 GLU624 ARG625 VAL626 CYS627 ARG628 LEU629 PHE630 THR631 ASN632 ASN633 LEU634 ASP635 ARG636 LEU637 ARG638 SER639 SER640 SER641 ALA642 ILE643 GLU644 ILE645 CYS646 PRO647 ASP648 ASP649 CYS650 GLU651 ASN652 GLU653 GLU654 ASP655 ARG656 GLU657 ILE658 ALA659 ARG660 GLN661 LEU662 GLN663 LEU664 ALA665 ILE666 GLY667 LYS668 VAL669 THR670 ALA671 ASP672 VAL673 GLU674 ARG675 PHE676 HIS677 PHE678 ASN679 ALA680 ALA681 ILE682 ALA683 ALA684 ILE685 MET686 SER687 VAL688 THR689 ASN690 LEU691 LEU692 TYR693 GLU694 LYS695 GLY696 GLY697 LYS698 ALA699 SER700 PRO701 THR702 VAL703 LEU704 ALA705 GLY706 SER707 LEU708 ARG709 LEU710 LEU711 VAL712 ARG713 LEU714 LEU715 ALA716 PRO717 PHE718 ALA719 PRO720 HIS721 ILE722 SER723 GLU724 GLU725 LEU726 TRP727 ALA728 LEU729 SER730 GLY731 CYS732 ASN733 SER734 LEU735 VAL736 ALA737 ALA738 GLU739 PRO740 TRP741 PRO742 THR743 ILE744 ASN745 GLU746 ARG747 LEU748 VAL749 GLN750 ALA751 GLU752 ASN753 ILE754 VAL755 LEU756 PRO757 VAL758 GLN759 ILE760 ASN761 GLY762 LYS763 LEU764 ILE765 ARG766 THR767 MET768 THR769 ILE770 PRO771 VAL772 ASN773 LEU774 ALA775 GLU776 GLU777 ASP778 ILE779 LEU780 SER781 THR782 VAL783 LEU784 ALA785 LEU786 PRO787 GLU788 VAL789 ARG790 SER791 ARG792 LEU793 SER794 ASP795 ARG796 ASP797 LEU798 LYS799 ASN800 TYR801 ARG802 TYR803 VAL804 PRO805 ASN806 ARG807 ILE808 ILE809 ASN810 LEU811 VAL812 VAL813 GLY814 LEU815 GLU816 HIS817
Nucleic acids
Unit 3 G1 C2 C3 C4 G5 C6 A7 U8 G9 G10 U11 G12 A13 A14 A15 U16 C17 G18 G19 U20 A20A A21 A22 C23 A24 C25 A26 U27 C28 G29 C30 A31 C32 A37 A38 U39 G40 C41 G42 C43 C44 G45 C46 C46A U46B C46C U46D G46E G46F C46G U47 U48 G49 C50 C51 G52 G53 U54 U55 C56 A57 A58 G59 U60 C61 C62 G63 G64 C65 U66 G67 C68 G69 G70 G71 C72 A73 C74 C75 A76
Unit 4 G1 C2 C3 C4 G5 C6 A7 U8 G9 G10 U11 G12 A13 A14 A15 U16 C17 G18 G19 U20 A20A A21 A22 C23 A24 C25 A26 U27 C28 G29 C30 A31 C32 U33 A37 A38 U39 G40 C41 G42 C43 C44 G45 C46 C46A U46B C46C U46D G46E G46F C46G U47 U48 G49 C50 C51 G52 G53 U54 U55 C56 A57 A58 G59 U60 C61 C62 G63 G64 C65 U66 G67 C68 G69 G70 G71 C72 A73 C74 C75 A76
Ligands
Unit 5 ZN900 LSS1818 SO41819
Unit 6 ZN900 LSS1818 SO41819 SO41820
Unit 7 MN1077 SO41078
Unit 8 MN1077 SO41078
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