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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURE OF MTR4, A DEXH HELICASE INVOLVED IN NUCLEAR RNA PROCESSING AND SURVEILLANCE
Keywords HYDROLASE-RNA COMPLEX, HYDROLASE, TRAMP, EXOSOME, DEAD, NUCLEOTIDE-BINDING
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2XGJ     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   ATP-DEPENDENT RNA HELICASE DOB1  A 964 7513 0
2  Protein   ATP-DEPENDENT RNA HELICASE DOB1  B 777 6024 0
3  RNA    C 5 107 0
4  RNA    D 5 110 0
5  Ligand   ATP-DEPENDENT RNA HELICASE DOB1  A 1 0 27
6  Ligand   ATP-DEPENDENT RNA HELICASE DOB1  B 1 0 27
7 Water     81 0 81
total       1834 13754 135
Proteins
Unit 1 MET80 LEU81 ALA82 ASP83 SER84 PHE85 GLU86 GLN87 GLU88 ALA89 SER90 ARG91 GLU92 VAL93 ASP94 ALA95 SER96 LYS97 GLY98 LEU99 THR100 ASN101 SER102 GLU103 THR104 LEU105 GLN106 VAL107 GLU108 GLN109 ASP110 GLY111 LYS112 VAL113 ARG114 LEU115 SER116 HIS117 GLN118 VAL119 ARG120 HIS121 GLN122 VAL123 ALA124 LEU125 PRO126 PRO127 ASN128 TYR129 ASP130 TYR131 THR132 PRO133 ILE134 ALA135 GLU136 HIS137 LYS138 ARG139 VAL140 ASN141 GLU142 ALA143 ARG144 THR145 TYR146 PRO147 PHE148 THR149 LEU150 ASP151 PRO152 PHE153 GLN154 ASP155 THR156 ALA157 ILE158 SER159 CYS160 ILE161 ASP162 ARG163 GLY164 GLU165 SER166 VAL167 LEU168 VAL169 SER170 ALA171 HIS172 THR173 SER174 ALA175 GLY176 LYS177 THR178 VAL179 VAL180 ALA181 GLU182 TYR183 ALA184 ILE185 ALA186 GLN187 SER188 LEU189 LYS190 ASN191 LYS192 GLN193 ARG194 VAL195 ILE196 TYR197 THR198 SER199 PRO200 ILE201 LYS202 ALA203 LEU204 SER205 ASN206 GLN207 LYS208 TYR209 ARG210 GLU211 LEU212 LEU213 ALA214 GLU215 PHE216 GLY217 ASP218 VAL219 GLY220 LEU221 MET222 THR223 GLY224 ASP225 ILE226 THR227 ILE228 ASN229 PRO230 ASP231 ALA232 GLY233 CYS234 LEU235 VAL236 MET237 THR238 THR239 GLU240 ILE241 LEU242 ARG243 SER244 MET245 LEU246 TYR247 ARG248 GLY249 SER250 GLU251 VAL252 MET253 ARG254 GLU255 VAL256 ALA257 TRP258 VAL259 ILE260 PHE261 ASP262 GLU263 VAL264 HIS265 TYR266 MET267 ARG268 ASP269 LYS270 GLU271 ARG272 GLY273 VAL274 VAL275 TRP276 GLU277 GLU278 THR279 ILE280 ILE281 LEU282 LEU283 PRO284 ASP285 LYS286 VAL287 ARG288 TYR289 VAL290 PHE291 LEU292 SER293 ALA294 THR295 ILE296 PRO297 ASN298 ALA299 MET300 GLU301 PHE302 ALA303 GLU304 TRP305 ILE306 CYS307 LYS308 ILE309 HIS310 SER311 GLN312 PRO313 CYS314 HIS315 ILE316 VAL317 TYR318 THR319 ASN320 PHE321 ARG322 PRO323 THR324 PRO325 LEU326 GLN327 HIS328 TYR329 LEU330 PHE331 PRO332 ALA333 HIS334 GLY335 ASP336 GLY337 ILE338 TYR339 LEU340 VAL341 VAL342 ASP343 GLU344 LYS345 SER346 THR347 PHE348 ARG349 GLU350 GLU351 ASN352 PHE353 GLN354 LYS355 ALA356 MET357 ALA358 SER359 ILE360 SER361 GLY392 ASP393 ILE394 TYR395 LYS396 ILE397 VAL398 LYS399 MET400 ILE401 TRP402 LYS403 LYS404 LYS405 TYR406 ASN407 PRO408 VAL409 ILE410 VAL411 PHE412 SER413 PHE414 SER415 LYS416 ARG417 ASP418 CYS419 GLU420 GLU421 LEU422 ALA423 LEU424 LYS425 MET426 SER427 LYS428 LEU429 ASP430 PHE431 ASN432 SER433 ASP434 ASP435 GLU436 LYS437 GLU438 ALA439 LEU440 THR441 LYS442 ILE443 PHE444 ASN445 ASN446 ALA447 ILE448 ALA449 LEU450 LEU451 PRO452 GLU453 THR454 ASP455 ARG456 GLU457 LEU458 PRO459 GLN460 ILE461 LYS462 HIS463 ILE464 LEU465 PRO466 LEU467 LEU468 ARG469 ARG470 GLY471 ILE472 GLY473 ILE474 HIS475 HIS476 SER477 GLY478 LEU479 LEU480 PRO481 ILE482 LEU483 LYS484 GLU485 VAL486 ILE487 GLU488 ILE489 LEU490 PHE491 GLN492 GLU493 GLY494 PHE495 LEU496 LYS497 VAL498 LEU499 PHE500 ALA501 THR502 GLU503 THR504 PHE505 SER506 ILE507 GLY508 LEU509 ASN510 MET511 PRO512 ALA513 LYS514 THR515 VAL516 VAL517 PHE518 THR519 SER520 VAL521 ARG522 LYS523 TRP524 ASP525 GLY526 GLN527 GLN528 PHE529 ARG530 TRP531 VAL532 SER533 GLY534 GLY535 GLU536 TYR537 ILE538 GLN539 MET540 SER541 GLY542 ARG543 ALA544 GLY545 ARG546 ARG547 GLY548 LEU549 ASP550 ASP551 ARG552 GLY553 ILE554 VAL555 ILE556 MET557 MET558 ILE559 ASP560 GLU561 LYS562 MET563 GLU564 PRO565 GLN566 VAL567 ALA568 LYS569 GLY570 MET571 VAL572 LYS573 GLY574 GLN575 ALA576 ASP577 ARG578 LEU579 ASP580 SER581 ALA582 PHE583 HIS584 LEU585 GLY586 TYR587 ASN588 MET589 ILE590 LEU591 ASN592 LEU593 MET594 ARG595 VAL596 GLU597 GLY598 ILE599 SER600 PRO601 GLU602 PHE603 MET604 LEU605 GLU606 HIS607 SER608 PHE609 PHE610 GLN611 PHE612 GLN613 ASN614 VAL615 ILE616 SER617 VAL618 PRO619 VAL620 MET621 GLU622 LYS623 LYS624 LEU625 ALA626 GLU627 LEU628 LYS629 LYS630 ASP631 PHE632 ASP633 GLY634 ILE635 GLU636 VAL637 GLU638 ASP639 GLU640 GLU641 ASN642 VAL643 LYS644 GLU645 TYR646 HIS647 GLU648 ILE649 GLU650 GLN651 ALA652 ILE653 LYS654 GLY655 TYR656 ARG657 GLU658 ASP659 VAL660 ARG661 GLN662 VAL663 VAL664 THR665 HIS666 PRO667 ALA668 ASN669 ALA670 LEU671 SER672 PHE673 LEU674 GLN675 PRO676 GLY677 ARG678 LEU679 VAL680 GLU681 ILE682 SER683 VAL684 ASN685 GLY686 LYS687 ASP688 ASN689 TYR690 GLY691 TRP692 GLY693 ALA694 VAL695 VAL696 ASP697 PHE698 ALA699 LYS700 ARG701 ILE702 ASN703 LYS704 ARG705 ASN706 PRO707 SER708 ALA709 VAL710 TYR711 THR712 ASP713 HIS714 GLU715 SER716 TYR717 ILE718 VAL719 ASN720 VAL721 VAL722 VAL723 ASN724 THR725 MET726 TYR727 ILE728 ASP729 SER730 PRO731 VAL732 ASN733 LEU734 LEU735 LYS736 PRO737 PHE738 ASN739 PRO740 THR741 LEU742 PRO743 GLU744 GLY745 ILE746 ARG747 PRO748 ALA749 GLU750 GLU751 GLY752 GLU753 LYS754 SER755 ILE756 CYS757 ALA758 VAL759 ILE760 PRO761 ILE762 THR763 LEU764 ASP765 SER766 ILE767 LYS768 SER769 ILE770 GLY771 ASN772 LEU773 ARG774 LEU775 TYR776 MET777 PRO778 LYS779 ASP780 ILE781 ARG782 ALA783 SER784 GLY785 GLN786 LYS787 GLU788 THR789 VAL790 GLY791 LYS792 SER793 LEU794 ARG795 GLU796 VAL797 ASN798 ARG799 ARG800 PHE801 PRO802 ASP803 GLY804 ILE805 PRO806 VAL807 LEU808 ASP809 PRO810 VAL811 LYS812 ASN813 MET814 LYS815 ILE816 GLU817 ASP818 GLU819 ASP820 PHE821 LEU822 LYS823 LEU824 MET825 LYS826 LYS827 ILE828 ASP829 VAL830 LEU831 ASN832 THR833 LYS834 LEU835 SER836 SER837 ASN838 PRO839 LEU840 THR841 ASN842 SER843 MET844 ARG845 LEU846 GLU847 GLU848 LEU849 TYR850 GLY851 LYS852 TYR853 SER854 ARG855 LYS856 HIS857 ASP858 LEU859 HIS860 GLU861 ASP862 MET863 LYS864 GLN865 LEU866 LYS867 ARG868 LYS869 ILE870 SER871 GLU872 SER873 GLN874 ALA875 VAL876 ILE877 GLN878 LEU879 ASP880 ASP881 LEU882 ARG883 ARG884 ARG885 LYS886 ARG887 VAL888 LEU889 ARG890 ARG891 LEU892 GLY893 PHE894 CYS895 THR896 PRO897 ASN898 ASP899 ILE900 ILE901 GLU902 LEU903 LYS904 GLY905 ARG906 VAL907 ALA908 CYS909 GLU910 ILE911 SER912 SER913 GLY914 ASP915 GLU916 LEU917 LEU918 LEU919 THR920 GLU921 LEU922 ILE923 PHE924 ASN925 GLY926 ASN927 PHE928 ASN929 GLU930 LEU931 LYS932 PRO933 GLU934 GLN935 ALA936 ALA937 ALA938 LEU939 LEU940 SER941 CYS942 PHE943 ALA944 PHE945 GLN946 GLU947 ARG948 CYS949 LYS950 GLU951 ALA952 PRO953 ARG954 LEU955 LYS956 PRO957 GLU958 LEU959 ALA960 GLU961 PRO962 LEU963 LYS964 ALA965 MET966 ARG967 GLU968 ILE969 ALA970 ALA971 LYS972 ILE973 ALA974 LYS975 ILE976 MET977 LYS978 ASP979 SER980 LYS981 ILE982 GLU983 VAL984 VAL985 GLU986 LYS987 ASP988 TYR989 VAL990 GLU991 SER992 PHE993 ARG994 HIS995 GLU996 LEU997 MET998 GLU999 VAL1000 VAL1001 TYR1002 GLU1003 TRP1004 CYS1005 ARG1006 GLY1007 ALA1008 THR1009 PHE1010 THR1011 GLN1012 ILE1013 CYS1014 LYS1015 MET1016 THR1017 ASP1018 VAL1019 TYR1020 GLU1021 GLY1022 SER1023 LEU1024 ILE1025 ARG1026 MET1027 PHE1028 LYS1029 ARG1030 LEU1031 GLU1032 GLU1033 LEU1034 VAL1035 LYS1036 GLU1037 LEU1038 VAL1039 ASP1040 VAL1041 ALA1042 ASN1043 THR1044 ILE1045 GLY1046 ASN1047 SER1048 SER1049 LEU1050 LYS1051 GLU1052 LYS1053 MET1054 GLU1055 ALA1056 VAL1057 LEU1058 LYS1059 LEU1060 ILE1061 HIS1062 ARG1063 ASP1064 ILE1065 VAL1066 SER1067 ALA1068 GLY1069 SER1070 LEU1071 TYR1072 LEU1073
Unit 2 HIS117 GLN118 VAL119 ARG120 HIS121 GLN122 VAL123 ALA124 LEU125 PRO126 PRO127 ASN128 TYR129 ASP130 TYR131 THR132 PRO133 ILE134 ALA135 GLU136 HIS137 LYS138 ARG139 VAL140 ASN141 GLU142 ALA143 ARG144 THR145 TYR146 PRO147 PHE148 THR149 LEU150 ASP151 PRO152 PHE153 GLN154 ASP155 THR156 ALA157 ILE158 SER159 CYS160 ILE161 ASP162 ARG163 GLY164 GLU165 SER166 VAL167 LEU168 VAL169 SER170 ALA171 HIS172 THR173 SER174 ALA175 GLY176 LYS177 THR178 VAL179 VAL180 ALA181 GLU182 TYR183 ALA184 ILE185 ALA186 GLN187 SER188 LEU189 LYS190 ASN191 LYS192 GLN193 ARG194 VAL195 ILE196 TYR197 THR198 SER199 PRO200 ILE201 LYS202 ALA203 LEU204 SER205 ASN206 GLN207 LYS208 TYR209 ARG210 GLU211 LEU212 LEU213 ALA214 GLU215 PHE216 GLY217 ASP218 VAL219 GLY220 LEU221 MET222 THR223 GLY224 ASP225 ILE226 THR227 ILE228 ASN229 PRO230 ASP231 ALA232 GLY233 CYS234 LEU235 VAL236 MET237 THR238 THR239 GLU240 ILE241 LEU242 ARG243 SER244 MET245 LEU246 TYR247 ARG248 GLY249 SER250 GLU251 VAL252 MET253 ARG254 GLU255 VAL256 ALA257 TRP258 VAL259 ILE260 PHE261 ASP262 GLU263 VAL264 HIS265 TYR266 MET267 ARG268 ASP269 LYS270 GLU271 ARG272 GLY273 VAL274 VAL275 TRP276 GLU277 GLU278 THR279 ILE280 ILE281 LEU282 LEU283 PRO284 ASP285 LYS286 VAL287 ARG288 TYR289 VAL290 PHE291 LEU292 SER293 ALA294 THR295 ILE296 PRO297 ASN298 ALA299 MET300 GLU301 PHE302 ALA303 GLU304 TRP305 ILE306 CYS307 LYS308 ILE309 HIS310 SER311 GLN312 PRO313 CYS314 HIS315 ILE316 VAL317 TYR318 THR319 ASN320 PHE321 ARG322 PRO323 THR324 PRO325 LEU326 GLN327 HIS328 TYR329 LEU330 PHE331 PRO332 ALA333 HIS334 GLY335 ASP336 GLY337 ILE338 TYR339 LEU340 VAL341 VAL342 ASP343 GLU344 LYS345 SER346 THR347 PHE348 ARG349 GLU350 GLU351 ASN352 PHE353 GLN354 LYS355 ALA356 MET357 ALA358 SER359 ILE360 SER361 LYS391 GLY392 ASP393 ILE394 TYR395 LYS396 ILE397 VAL398 LYS399 MET400 ILE401 TRP402 LYS403 LYS404 LYS405 TYR406 ASN407 PRO408 VAL409 ILE410 VAL411 PHE412 SER413 PHE414 SER415 LYS416 ARG417 ASP418 CYS419 GLU420 GLU421 LEU422 ALA423 LEU424 LYS425 MET426 SER427 LYS428 LEU429 ASP430 PHE431 ASN432 SER433 ASP434 ASP435 GLU436 LYS437 GLU438 ALA439 LEU440 THR441 LYS442 ILE443 PHE444 ASN445 ASN446 ALA447 ILE448 ALA449 LEU450 LEU451 PRO452 GLU453 THR454 ASP455 ARG456 GLU457 LEU458 PRO459 GLN460 ILE461 LYS462 HIS463 ILE464 LEU465 PRO466 LEU467 LEU468 ARG469 ARG470 GLY471 ILE472 GLY473 ILE474 HIS475 HIS476 SER477 GLY478 LEU479 LEU480 PRO481 ILE482 LEU483 LYS484 GLU485 VAL486 ILE487 GLU488 ILE489 LEU490 PHE491 GLN492 GLU493 GLY494 PHE495 LEU496 LYS497 VAL498 LEU499 PHE500 ALA501 THR502 GLU503 THR504 PHE505 SER506 ILE507 GLY508 PRO512 ALA513 LYS514 THR515 VAL516 VAL517 PHE518 THR519 SER520 VAL521 VAL532 SER533 GLY534 GLY535 GLU536 TYR537 ILE538 GLN539 MET540 SER541 GLY542 ARG543 ALA544 GLY545 ARG546 ARG547 GLY548 LEU549 ASP550 ASP551 ARG552 GLY553 ILE554 VAL555 ILE556 MET557 MET558 ILE559 ASP560 GLU561 LYS562 MET563 GLU564 PRO565 GLN566 VAL567 ALA568 LYS569 GLY570 MET571 VAL572 LYS573 GLY574 GLN575 ALA576 ASP577 ARG578 LEU579 ASP580 SER581 ALA582 PHE583 HIS584 LEU585 GLY586 TYR587 ASN588 MET589 ILE590 LEU591 ASN592 LEU593 MET594 ARG595 VAL596 GLU597 GLY598 ILE599 SER600 PRO601 GLU602 PHE603 MET604 LEU605 GLU606 HIS607 SER608 PHE609 PHE610 GLN611 PHE612 GLN613 ASN614 VAL615 ILE616 SER617 VAL618 PRO619 VAL620 MET621 GLU622 LYS623 LYS624 LEU625 ALA626 GLU627 LEU628 LYS629 LYS630 ASP631 PHE632 ASP633 GLY634 ILE635 GLU636 VAL637 GLU638 ASP639 GLU640 GLU641 ASN642 VAL643 LYS644 GLU645 TYR646 HIS647 GLU648 ILE649 GLU650 GLN651 ALA652 ILE653 LYS654 GLY655 TYR656 ARG657 GLU658 ASP659 VAL660 ARG661 GLN662 VAL663 VAL664 THR665 HIS666 PRO667 ALA668 ASN669 ALA670 LEU671 PRO810 VAL811 LYS812 ASN813 MET814 LYS815 ILE816 GLU817 ASP818 GLU819 ASP820 PHE821 LEU822 LYS823 LEU824 MET825 LYS826 LYS827 ILE828 ASP829 VAL830 LEU831 ASN832 THR833 LYS834 LEU835 SER836 SER837 ASN838 PRO839 LEU840 THR841 ASN842 SER843 MET844 ARG845 LEU846 GLU847 GLU848 LEU849 TYR850 GLY851 LYS852 TYR853 SER854 ARG855 LYS856 HIS857 ASP858 LEU859 HIS860 GLU861 ASP862 MET863 LYS864 GLN865 LEU866 LYS867 ARG868 LYS869 ILE870 SER871 GLU872 SER873 GLN874 ALA875 VAL876 ILE877 GLN878 LEU879 ASP880 ASP881 LEU882 ARG883 ARG884 ARG885 LYS886 ARG887 VAL888 LEU889 ARG890 ARG891 LEU892 GLY893 PHE894 CYS895 THR896 PRO897 ASN898 ASP899 ILE900 ILE901 GLU902 LEU903 LYS904 GLY905 ARG906 VAL907 ALA908 CYS909 GLU910 ILE911 SER912 SER913 GLY914 ASP915 GLU916 LEU917 LEU918 LEU919 THR920 GLU921 LEU922 ILE923 PHE924 ASN925 GLY926 ASN927 PHE928 ASN929 GLU930 LEU931 LYS932 PRO933 GLU934 GLN935 ALA936 ALA937 ALA938 LEU939 LEU940 SER941 CYS942 PHE943 ALA944 PHE945 GLN946 GLU947 ARG948 CYS949 LYS950 GLU951 ALA952 PRO953 ARG954 LEU955 LYS956 PRO957 GLU958 LEU959 ALA960 GLU961 PRO962 LEU963 LYS964 ALA965 MET966 ARG967 GLU968 ILE969 ALA970 ALA971 LYS972 ILE973 ALA974 LYS975 ILE976 MET977 LYS978 ASP979 SER980 LYS981 ILE982 GLU983 VAL984 VAL985 GLU986 LYS987 ASP988 TYR989 VAL990 GLU991 SER992 PHE993 ARG994 HIS995 GLU996 LEU997 MET998 GLU999 VAL1000 VAL1001 TYR1002 GLU1003 TRP1004 CYS1005 ARG1006 GLY1007 ALA1008 THR1009 PHE1010 THR1011 GLN1012 ILE1013 CYS1014 LYS1015 MET1016 THR1017 ASP1018 VAL1019 TYR1020 GLU1021 GLY1022 SER1023 LEU1024 ILE1025 ARG1026 MET1027 PHE1028 LYS1029 ARG1030 LEU1031 GLU1032 GLU1033 LEU1034 VAL1035 LYS1036 GLU1037 LEU1038 VAL1039 ASP1040 VAL1041 ALA1042 ASN1043 THR1044 ILE1045 GLY1046 ASN1047 SER1048 SER1049 LEU1050 LYS1051 GLU1052 LYS1053 MET1054 GLU1055 ALA1056 VAL1057 LEU1058 LYS1059 LEU1060 ILE1061 HIS1062 ARG1063 ASP1064 ILE1065 VAL1066 SER1067 ALA1068 GLY1069 SER1070 LEU1071 TYR1072 LEU1073
Nucleic acids
Unit 3 A1 A2 A3 A4 A5
Unit 4 A1 A2 A3 A4 A5
Ligands
Unit 5 ADP2074
Unit 6 ADP2074
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