Comparison of RNA 3D Structures

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Structure Alignment of 3u5h8,5 and 1s720 (Note: If JSmol does not show the alignment, please refresh this page by F5)

Structure Overlap
RMSD
Fragment Score
Topology Score
#C3' atoms of 3u5h8,5
#C3' atoms of 1s720
Match Size
#Identical Residues
#Identical Residues with Heuristics
89.01%
1.70
0.99
0.95
3308
2749
2447
1320
1316

Alignment

                       10        20        30        40        50        60        70        80        90        100       110       120                     10        20                           10        20        30        40                             10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180                    10                              10                                          10        20        30        40        50        60        70        80        90        100       110       120                         10        20                      10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200                             10        20        30                      10        20                                            10        20        30        40        50        60        70        80        90        100       110       120                       10                       10        20        30        40        50                             10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200                        10        20        30        40                     10        20        30        40        50        60        70        80        90        100       110                         10        20        30                             10        20        30        40        50        60        70        80        90        100       110       120       130                      10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160                    10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170                        10                       10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590                     10        20        30        40        50                          10        20        30        40                          10        20        30        40        50        60        70        80        90        100       110       120                            10      
3u5h8,5   135:AUCAGGUAGGAG-UACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGAAAAGAAACCA-AC-C-GGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUU-GAAAUCUGG:1285   1425:CGAGUUGUAAUUUGGA-G-A-G--GG:1625   1845:UCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUG:2315   2545:AAG-U-G-C-CUUC-G--AAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAA---GUGGGUGGUAA-A-U-UCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUGAUGGAAAGAUGAAAAGAACUUUGAA-AAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAG:4195   4245:GGGCAUUUGAUC-A----G:4375   4995:GC-A-U-C-AGUUUU:5095   5845:GAC:5865   6165:GGCAUAA-U--GGUU-AUAUGCCGCCCGUCUUGAAACACGGACCAAGGAGUCUAACGUCUAUGCGAGUGUU-UGGGUGUAAAACCCA-U-ACGCGUAAUGAAAGUGAA-C-GUAGGUUGGGGCCU:7315   7385:AGGUGCACAAUCGACCGAUCC:7585   7755:AUUUGA-GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCCAG-A-G-GAAA-C-U---CUGGUGGAGGCUCGU-AGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCUCAGGAUAGCAGAA:9735   9805:AUCAGUUUUAUGAGGUAAAGCGAAUGAUUAG:10105 10415:U-UCUCAAACUUUAAAUAUGUAA:10625 10985:AAUGAAG:11045 11095:UUUAGUGGGCCAUUUUUGGUAAGCAGAACUGGCGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAU-CAGACACC---ACAAAAGGUGUUAGUUCAUCUAGA---C:12245 12545:CC-G-C-UAAGG:12625 12885:UGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGCGUGUUACCUAUACUCUACCGUCAGG:13455 13565:UGCCCUGA--CGAGUAGGCAGGCGUGGAGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUGGUGGUAGUAGCAA--AUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAG-AUGGGGAAGC-UCCGU:15535 15835:AUCGAA-AGGGAAUCCGGUUAAGAUUCCGGAACCUGGAUA:16215 16455:UGA-A-U-GUGGAGACGUCGGCGCGAGCCCUGGGAGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUUA-UGGCUGGAA-GAGG:17545 17715:CUCCGGUG-C-GCUUGU--GACGGCCCGUGAAAAUC-C:18035 18215:UCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCC-AAGGUGAACAGCCUCUAGUUG-AUAGAA-UAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAG-G:19485 21005:AC--UUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUGGUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAA----UUCAACCAAGCGCGGGUAAACGGCGGGAG:22535 22665:UCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAAACCACA--GCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUG:24375 25085:UUUACUUAUUCA:25195 25875:UU-GAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGAUAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGGUAAAAGCCCCCUUGAUUUUGAUUU-UC---AGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUCGAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCAGUCAAGCG-UUCAUAGC-GACAUUGCUUUUUGAUUCUUCGAUGUCGGCUCUUCCUAUCAUACCGAAGCAGAAU-UCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAU-----GUUACCGCAAUAGU-AAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGCGGCUGUCUGAUCAGGCAU-UGCCGCGAAGCUACCAUCCGC-U--GGAUUAUGGCUGAACGCCUCUAAGUCAGAAUCCAUGCUAG-AA-C--GCGGU-GA---U:31515 32955:AAUCAUUUGUAUACGACUUAGAUGUAC-A--ACGGGGUAUUGUAAGCAGUAGAGU:33465 33595:ACGAUCUGCUGAGAUUA-AGCCUUU-G-UUGU--CUG-A-U-UUG:33955    18:AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAUACGUAAUG-UGA-AUU----GCAGAA-U-UCCGU-G-AAUCAUCGAAUCUUUGAACGCACA-U-UG-C:1158   1368:GC-AUGCCUGU:1458 
1s720    1400:GC-GCAAUGAGGAA-CCCCGAGAACUGAAACAUCUCAGUAUCGGGAGGAACAGAAAACGCA-A-UGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCAAACC-G--AAGCCCU:2530   2580:GGCAAUGUGGUGUCA-G-G-G-CUAC:2790   3020:ACGAAGUCUCUUGGAACAGAGCGUGAUACAGGGUGACAACCCCGUACU:3490   3660:UG-C-G-G-U-AG-U-GCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAAC-GCA-GG-C-A-U-CGACUGCGAAGGCUAAACAC-AACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCUGCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCG:5310   5380:CGACAGGGCAU-A-CAAGG:5540   5600:C-G-A-C-G-AAUGA:5690   5910:AGA:5930   5990:GGG--A-A-GCCGAUGUUCUGUCGUACGUUUUG-AAAACGAGCCAGGGAGUGUGUCUGCAUGGCAAGUCU-AACCGGAGUAUCCGG-G-GAGGCACAGGGAAACCGA-C-A--UGGCCGCAGGGC:7120   7160:GCCCGAGGGC-CGCCGUCUUC:7350   7370:AGGGC-GG-G-GAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUACGCAUGGACAAGAUGAAGCGU-G-C-C--G-A-A-AGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUACAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUGGUUCCAAUCGAAACAUGUCGAAGCAUGACCUCC:9340   9390:AGGUAGUCUGUGAGGUAGAGCGACCGAUUGG:9690   9990:CCUGUCAAACUCCAAACUUACAG:10210 10220:ACGCC-G:10270 10370:GGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACAACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAA-G-UGUAAU-CCUCUGAAGGUGGUCUCGAGCC----CUAGA:11520 11840:C-U-C-U--AAG:11900 12170:GUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGACCUGUCCGUACCA:12740 12790:UACUGGUAAUCGAGUAGAUUGGCGCUCUAAUU-GGAUGGAAGUAG-GGGUGAAAACUCCUAUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUAGUCGGGUGAGAACCCCGACGGCCU-AAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUGAGGGUUAGCCGGUCCUAAGUCAUA-CCGCAACUCGACU:14780 14810:GACGAAAUGGGAAACGGGUUAAUAUUCCCGUGCCACUAUG:15200 15240:UG-A-A-A--GUUGACGCCCUGGGGUCGAUCACGCUGGGCA-UCG-CCCAGUCGAACCGUCCAACUCCGUGGAA-GCCGUAAUGGCAGGAAGCGGACGAACGGCG-GCA-UAGGG:16290 16320:ACGUGAU-U-C---AA-CCUGGGGCCCAUGAAAAGACG:16630 16650:G-CAUAGUGUCCGUACCGAGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUUAGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGG:17950 17970:A-CGGAGCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUCCGCAA-GGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAG-GUAUCUGAACACCUCG-U-ACAAGAGGACGAAGGACCUGUCAACGGCGGGGG:19510 19640:UCUUAAGGUAGCGUAGUACCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACGUUGGGCCCGGUGAACUGUA-CAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAAGACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAG:21360 22380:ACUCU-CACUCC:22480 22510:GAGGAGGACACCGAUAGCCGGGCAGUUUGACUGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGCUAUCUCAGCCGGG-----GACCCGGCGAAGAGUGCAAGAGCAAAAGAUAGCUUGACAGUGUUCUUC-CCAA-CGAGGAACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAG-CCUGCUUGAUGCGGGCAAUUGAUGACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCA-CAUAU-CGACCGAGUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGG-CAAGGGUGAGGU--UUCGCCUAUUAAAGGAGGUCGUGAGCUGGG-U-AGACCGUCGUGAGACAGGUCGGCUGCUAUCUACUGGGUGU-GUAAGG-GUGUCUGACAAGAACGACCGUAUAGUACGAGAGGAACUACGGUUGGUGGCCACUGGUGUA-CCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCA-CGCCAC-A-CGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAA-A-AGAGACACC-GCCG:28260 28280:GGUCCCGCGUACAAGACGCGG-UC-G-A-UAGACUCGGGGUGUGCGCGU-CGAGG:28770 28800:ACGAGACGUUAAGCCC-A--CGAG-C-A-CU-AACA-G-A-CCAA:29140   100:U-AUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAGCUGCGAUAAGCCAUGGGGAGCC-GCACGGAGG-C-GA--A-G-A-A-CCAUGGAUUUCCGAAUGAGA-A-UC-UC:1240   1290:A-CAAUUGCUU:1380 

Alignment in PIR format Matched residue pairs Superimposed structures

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