RNA 3D Hub //

5DM8 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5DM8_0011/X/59:68Pseudoknot with intercalation
geometric
HL_7A0S_001
HL_17803.2
HL_5DM8_0021/X/86:97No text annotation
geometric
HL_7A0S_002
HL_76590.1
HL_5DM8_0031/X/123:128No text annotation
geometric
HL_5J7L_143
NA
HL_5DM8_0041/X/135:140GNRA
geometric
HL_3V7E_003
NA
HL_5DM8_0051/X/148:153GNRA
geometric
HL_3NDB_002
NA
HL_5DM8_0061/X/165B:180No text annotation
HL_5DM8_0071/X/197:202No text annotation
geometric
HL_7A0S_007
HL_91813.1
HL_5DM8_0081/X/218:224No text annotation
geometric
HL_7RQB_008
NA
HL_5DM8_0091/X/305:312T-loop with 1 bulged base
geometric
HL_7A0S_010
HL_13999.4
HL_5DM8_0101/X/319:323No text annotation
geometric
HL_7A0S_011
HL_75660.9
HL_5DM8_0111/X/327:335T-loop with unstacked turn
geometric
HL_5J7L_144
NA
HL_5DM8_0121/X/382:392No text annotation
geometric
HL_7A0S_013
HL_91503.8
HL_5DM8_0131/X/410:417Pseudoknot geometry
geometric
HL_7A0S_014
HL_30680.5
HL_5DM8_0141/X/462:467GNRA
geometric
HL_3G9C_008
NA
HL_5DM8_0151/X/487:493GNRA
geometric
HL_7A0S_016
HL_34789.5
HL_5DM8_0161/X/544:549Mini UNCG with extended bulge
geometric
HL_7A0S_017
HL_90436.4
HL_5DM8_0171/X/566:575T-loop with 2 stacked bulged bases
geometric
HL_7A0S_018
HL_33597.4
HL_5DM8_0181/X/611:616No text annotation
geometric
HL_5TBW_075
NA
HL_5DM8_0191/X/629:634GNRA
geometric
HL_7A0S_020
HL_34789.5
HL_5DM8_0201/X/640:647tRNA anticodon loop
geometric
HL_5UD5_002
HL_87306.2
HL_5DM8_0211/X/712:719No text annotation
geometric
HL_5TBW_006
NA
HL_5DM8_0221/X/744:753No text annotation
geometric
HL_7A0S_022
HL_50204.2
HL_5DM8_0231/X/779:785No text annotation
geometric
HL_7RQB_024
NA
HL_5DM8_0241/X/826:831No text annotation
geometric
HL_7RQB_025
NA
HL_5DM8_0261/X/955:962GNRA
geometric
HL_7A0S_026
HL_34789.5
HL_5DM8_0271/X/978:985No text annotation
geometric
HL_5TBW_006
NA
HL_5DM8_0281/X/1064:1074No text annotation
geometric
HL_6PRV_001
HL_20174.1
HL_5DM8_0291/X/1092:1099GNRA with tandem sheared
geometric
HL_5J7L_154
NA
HL_5DM8_0301/X/1172B:1175No text annotation
HL_5DM8_0311/X/1222:1227GNRA
geometric
HL_7A0S_031
HL_34789.5
HL_5DM8_0321/X/1281:1289T-loop with 2 stacked bulged bases
geometric
HL_4WF9_032
HL_33597.4
HL_5DM8_0331/X/1324:1330Pseudoknot geometry with 3' bulge
geometric
HL_7A0S_033
HL_49081.1
HL_5DM8_0341/X/1363:1368GNRA variation
geometric
HL_7A0S_034
HL_34789.5
HL_5DM8_0351/X/1389:1398No text annotation
geometric
HL_7A0S_035
HL_77449.2
HL_5DM8_0361/X/1451:1461Pseudoknot
homologous
HL_7A0S_036
HL_00824.1
HL_5DM8_0371/X/1492:1498Pseudoknot geometry with 3' bulge
geometric
HL_4WF9_033
HL_49081.1
HL_5DM8_0381/X/1533:1538No text annotation
geometric
HL_4WF9_003
HL_75660.9
HL_5DM8_0391/X/1565:1568Mini UNCG
geometric
HL_5J7L_172
NA
HL_5DM8_0401/X/1612:1619No text annotation
geometric
HL_7A0S_040
HL_28592.3
HL_5DM8_0411/X/1630:1635No text annotation
geometric
HL_7RQB_041
NA
HL_5DM8_0421/X/1691:1696UNCG
geometric
HL_4LFB_011
HL_61337.5
HL_5DM8_0431/X/1734:1738No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_5DM8_0441/X/1746:1750No text annotation
geometric
HL_7A0S_044
HL_80709.5
HL_5DM8_0451/X/1776:1788No text annotation
geometric
HL_7A0S_045
HL_50951.2
HL_5DM8_0461/X/1806:1811GNRA
geometric
HL_7A0S_046
HL_93535.3
HL_5DM8_0471/X/1864:1878GNRA
geometric
HL_5TBW_059
NA
HL_5DM8_0491/X/1949:1957No text annotation
geometric
HL_7RQB_049
NA
HL_5DM8_0501/X/2027:2036No text annotation
geometric
HL_7A0S_049
HL_78372.2
HL_5DM8_0511/X/2141:2150No text annotation
geometric
HL_2ZZM_002
HL_33487.2
HL_5DM8_0521/X/2205:2217No text annotation
homologous
HL_7A0S_051
HL_38046.1
HL_5DM8_0531/X/2248:2256LSU P loop
geometric
HL_7A0S_052
HL_11974.3
HL_5DM8_0541/X/2264:2276No text annotation
geometric
HL_7A0S_053
HL_02042.2
HL_5DM8_0561/X/2324:2331Pseudoknot geometry
geometric
HL_7A0S_055
HL_52651.3
HL_5DM8_0571/X/2355:2362GNRA with extra cWW
geometric
HL_7A0S_056
HL_87268.3
HL_5DM8_0581/X/2374:2379GNRA
geometric
HL_7A0S_057
HL_34789.5
HL_5DM8_0591/X/2404:2413No text annotation
geometric
HL_7A0S_058
HL_51853.2
HL_5DM8_0601/X/2471:2479No text annotation
geometric
HL_5J7L_193
NA
HL_5DM8_0611/X/2528:2535GNRA variation
geometric
HL_7A0S_060
HL_46665.3
HL_5DM8_0621/X/2551:2557LSU A loop
geometric
HL_7A0S_061
HL_48677.2
HL_5DM8_0631/X/2594:2599GNRA
geometric
HL_7A0S_062
HL_34789.5
HL_5DM8_0641/X/2658:2663GNRA
geometric
HL_5FJC_002
HL_34789.5
HL_5DM8_0651/X/2701:2706Ribsomal LSU H95
geometric
HL_7A0S_064
HL_12125.3
HL_5DM8_0661/X/2745:2759No text annotation
geometric
HL_7RQB_066
NA
HL_5DM8_0671/X/2793:2799No text annotation
HL_5DM8_0681/X/2819:2827No text annotation
geometric
HL_7A0S_067
HL_37889.2
HL_5DM8_0691/X/2856:2861GNRA
geometric
HL_7A0S_068
HL_34789.5
HL_5DM8_0701/Y/40:46No text annotation
geometric
HL_5J7L_203
NA
HL_5DM8_0711/Y/88:93GNRA
geometric
HL_5J7L_191
NA

Problematic loops

#loop idProblemSequence
HL_5DM8_025No text annotation
HL_5DM8_048No text annotation
HL_5DM8_055No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5DM8_0011/X/24:30,
1/X/510:516		Triple sheared with non-canonical cWW
geometric
IL_4WF9_001
IL_22311.2
IL_5DM8_0021/X/36:37,
1/X/442:444		Single bulged A
geometric
IL_7A0S_002
IL_14190.3
IL_5DM8_0041/X/81:85,
1/X/98:105		Kink-turn
geometric
IL_7A0S_004
IL_94910.1
IL_5DM8_0051/X/162:163,
1/X/184:186		Single stack bend
geometric
IL_4WF9_007
IL_15011.4
IL_5DM8_0061/X/210:217,
1/X/225:231		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_007
IL_62167.4
IL_5DM8_0071/X/292:295,
1/X/343:348		No text annotation
geometric
IL_7A0S_008
IL_05192.8
IL_5DM8_0081/X/481:484,
1/X/496:509		No text annotation
geometric
IL_7A0S_009
IL_44923.2
IL_5DM8_0091/X/542:544,
1/X/549:551		No text annotation
IL_5DM8_0101/X/564:566,
1/X/575:577		Isolated non-canonical cWW pair
geometric
IL_7A0S_011
IL_71625.4
IL_5DM8_0111/X/591:592A,
1/X/665:666		Single bulged A
geometric
IL_2C4Q_001
IL_14190.3
IL_5DM8_0121/X/605:609,
1/X/618:622		AAA cross-strand stack
geometric
IL_7RQB_016
NA
IL_5DM8_0131/X/672:674,
1/X/806:808		Isolated non-canonical cWW pair
geometric
IL_5J7L_259
NA
IL_5DM8_0141/X/674:678,
1/X/799:806		tHW-tHW cross-strand stack
geometric
IL_7A0S_015
IL_73855.2
IL_5DM8_0151/X/697:698,
1/X/763:765		Single bulged A
geometric
IL_7A0S_016
IL_14190.3
IL_5DM8_0161/X/702:703,
1/X/728:730		Single bulged G
geometric
IL_7RQB_020
NA
IL_5DM8_0171/X/703:708,
1/X/723:728		Triple sheared with non-canonical cWW
geometric
IL_7A0S_018
IL_29495.2
IL_5DM8_0181/X/738:741,
1/X/756:758		Major groove platform with extra cWW
geometric
IL_7A0S_019
IL_36931.3
IL_5DM8_0191/X/741:743,
1/X/754:756		Isolated non-canonical cWW pair
geometric
IL_7A0S_020
IL_01003.5
IL_5DM8_0201/X/775:777,
1/X/787:791		Multiple bulged bases
geometric
IL_7RQB_023
NA
IL_5DM8_0211/X/837:838,
1/X/940:942		Single stack bend
geometric
IL_7A0S_022
IL_15011.4
IL_5DM8_0231/X/850:851,
1/X/927:929		Single bulged C
geometric
IL_7A0S_025
IL_05642.4
IL_5DM8_0241/X/851:853,
1/X/925:927		Isolated non-canonical cWW pair
geometric
IL_7A0S_026
IL_01003.5
IL_5DM8_0251/X/858:862,
1/X/915:920		5x5 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_7RQB_027
NA
IL_5DM8_0261/X/862:863,
1/X/913:915		Minor groove platform
geometric
IL_7A0S_028
IL_34520.4
IL_5DM8_0271/X/864:868,
1/X/909:912		C-loop
geometric
IL_4WF9_033
IL_16301.2
IL_5DM8_0291/X/952:954,
1/X/963:965		No text annotation
geometric
IL_7RQB_034
NA
IL_5DM8_0301/X/994:996,
1/X/1159:1160		Single bulged C
geometric
IL_7A0S_032
IL_05642.4
IL_5DM8_0321/X/1004:1011,
1/X/1150:1151		SSU/LSU pseudoknot
geometric
IL_7A0S_034
IL_46868.1
IL_5DM8_0331/X/1011:1013,
1/X/1149:1150		Single bulged U
geometric
IL_5J7L_279
NA
IL_5DM8_0341/X/1018:1024,
1/X/1139:1144		Kink-turn related
geometric
IL_5J7L_280
NA
IL_5DM8_0351/X/1024:1030,
1/X/1124:1139		No text annotation
geometric
IL_7A0S_037
IL_50715.4
IL_5DM8_0361/X/1031:1034,
1/X/1121:1123		Isolated non-canonical cWW pair
geometric
IL_7RQB_041
NA
IL_5DM8_0381/X/1059:1062,
1/X/1076:1079		No text annotation
geometric
IL_1MMS_001
NA
IL_5DM8_0391/X/1087:1091,
1/X/1100:1102		Major groove platform with extra cWW
geometric
IL_7RQB_022
NA
IL_5DM8_0401/X/1164:1167,
1/X/1182:1185		Tandem non-canonical cWW pairs
geometric
IL_7A0S_040
IL_71194.3
IL_5DM8_0411/X/1196:1198,
1/X/1247:1250		Isolated cWS basepair
geometric
IL_7A0S_041
IL_42997.6
IL_5DM8_0421/X/1204:1206,
1/X/1239:1241		Isolated non-canonical cWW pair
geometric
IL_7A0S_042
IL_01003.5
IL_5DM8_0431/X/1208:1215,
1/X/1234:1238		Kink-turn
geometric
IL_7A0S_043
IL_90775.2
IL_5DM8_0441/X/1219:1221,
1/X/1228:1230		Intercalated cWW
geometric
IL_7A0S_044
IL_53541.1
IL_5DM8_0451/X/1262:1269,
1/X/2011:2017		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7RQB_049
NA
IL_5DM8_0461/X/1310:1313,
1/X/1603:1604		Major groove platform; stack outside cWW
geometric
IL_5J7L_290
NA
IL_5DM8_0481/X/1351:1355,
1/X/1376:1380		UAA/GAN
geometric
IL_7A0S_048
IL_89021.4
IL_5DM8_0491/X/1357:1361,
1/X/1370:1374		tSH-tWH-tHS
geometric
IL_7A0S_049
IL_05821.2
IL_5DM8_0501/X/1412:1416,
1/X/1582:1589		Kink-turn
geometric
IL_7A0S_050
IL_28245.1
IL_5DM8_0511/X/1417:1421,
1/X/1577:1581		UAA/GAN
geometric
IL_7A0S_051
IL_08938.2
IL_5DM8_0521/X/1433:1435,
1/X/1557:1560		Isolated tWW turn
geometric
IL_7RQB_056
NA
IL_5DM8_0531/X/1437:1440,
1/X/1551:1555		tSH-tHW
geometric
IL_7A0S_053
IL_74317.1
IL_5DM8_0541/X/1448:1450,
1/X/1462:1463		Single stack bend
geometric
IL_7A0S_054
IL_15011.4
IL_5DM8_0551/X/1473:1474,
1/X/1518:1519		Single bulged C
geometric
IL_5TBW_069
NA
IL_5DM8_0561/X/1475:1478,
1/X/1514:1517		Double sheared
geometric
IL_4WF9_087
IL_58355.3
IL_5DM8_0571/X/1481:1483,
1/X/1505:1511		No text annotation
IL_5DM8_0581/X/1487:1491,
1/X/1499:1501		No text annotation
IL_5DM8_0591/X/1651:1656,
1/X/2004:2006		No text annotation
geometric
IL_7A0S_059
IL_12566.5
IL_5DM8_0601/X/1663:1665,
1/X/1995:1997		Isolated tWW turn
geometric
IL_7A0S_060
IL_10432.2
IL_5DM8_0611/X/1666:1669,
1/X/1993:1994		Major groove platform; stack outside cWW
geometric
IL_7A0S_061
IL_74641.3
IL_5DM8_0621/X/1669:1674,
1/X/1990:1993		Intercalated tWH
geometric
IL_7A0S_062
IL_28217.2
IL_5DM8_0631/X/1686:1691,
1/X/1696:1702		tSH-tSH-tHH-tHS
geometric
IL_5TBW_078
NA
IL_5DM8_0641/X/1770:1771,
1/X/1980:1982		Single bulged A
geometric
IL_7A0S_064
IL_14190.3
IL_5DM8_0651/X/1798:1804,
1/X/1813:1821		Kink-turn related
geometric
IL_5J7L_313
NA
IL_5DM8_0661/X/1837:1840,
1/X/1902:1903		Minor groove platform, major groove intercalation
geometric
IL_7A0S_066
IL_55206.2
IL_5DM8_0671/X/1841:1842,
1/X/1898:1901		Major groove intercalation
geometric
IL_5J7L_315
NA
IL_5DM8_0681/X/1846:1849,
1/X/1893:1894		Major groove minor groove platform; mini C-loop
geometric
IL_5J7L_316
NA
IL_5DM8_0691/X/1850:1855,
1/X/1887:1892		No text annotation
geometric
IL_9E6Q_072
IL_74322.2
IL_5DM8_0701/X/1856:1860,
1/X/1882:1886		Triple sheared
geometric
IL_7RQB_075
NA
IL_5DM8_0711/X/1933:1934,
1/X/1964:1967		Bulged stacked bases
geometric
IL_5J7L_318
NA
IL_5DM8_0721/X/1934:1945,
1/X/1961:1964		No text annotation
geometric
IL_7A0S_072
IL_04332.3
IL_5DM8_0731/X/2050:2052,
1/X/2617:2618		Major groove platform
geometric
IL_7RQB_078
NA
IL_5DM8_0741/X/2054:2057,
1/X/2611:2615		No text annotation
geometric
IL_7A0S_074
IL_70335.1
IL_5DM8_0751/X/2067:2069,
1/X/2442:2443		Single bulged U
geometric
IL_7A0S_075
IL_97561.6
IL_5DM8_0761/X/2070:2071,
1/X/2438:2441		Minor groove platform
geometric
IL_7A0S_076
IL_34520.4
IL_5DM8_0771/X/2081:2083,
1/X/2236:2239		Isolated tHS basepair with bulges
geometric
IL_7A0S_077
IL_87316.3
IL_5DM8_0781/X/2085:2087,
1/X/2232:2234		Isolated non-canonical cWW pair
geometric
IL_7A0S_078
IL_71625.4
IL_5DM8_0791/X/2108:2110,
1/X/2179:2181		No text annotation
IL_5DM8_0801/X/2110:2120,
1/X/2178:2179		No text annotation
IL_5DM8_0831/X/2297:2299,
1/X/2317:2321		Isolated tHS basepair with bulges
geometric
IL_5TBW_099
NA
IL_5DM8_0841/X/2350:2353,
1/X/2364:2367		Double sheared
geometric
IL_7RQB_089
NA
IL_5DM8_0851/X/2401:2403,
1/X/2414:2415		Major groove platform
geometric
IL_1XJR_002
IL_48076.9
IL_5DM8_0861/X/2453:2454,
1/X/2498:2500		Single stack bend
geometric
IL_7A0S_083
IL_15011.4
IL_5DM8_0871/X/2454:2455,
1/X/2496:2498		Major groove platform
geometric
IL_4WF9_090
IL_48076.9
IL_5DM8_0891/X/2459:2461,
1/X/2489:2493		Major groove minor groove platform with extra cWW
geometric
IL_7A0S_086
IL_36931.3
IL_5DM8_0901/X/2466:2470,
1/X/2480:2484		Double sheared with non-canonical cWW
geometric
IL_7A0S_087
IL_87767.3
IL_5DM8_0911/X/2510:2512,
1/X/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_4WF9_095
IL_68118.5
IL_5DM8_0921/X/2512:2513,
1/X/2571:2574		Multiple bulged bases
geometric
IL_7A0S_090
IL_44609.3
IL_5DM8_0931/X/2522:2523,
1/X/2540:2543		Major groove platform with intercalation
geometric
IL_7A0S_091
IL_94991.2
IL_5DM8_0941/X/2591:2592,
1/X/2601:2603		Single bulged A
geometric
IL_7RQB_101
NA
IL_5DM8_0951/X/2636:2640,
1/X/2774:2782		tSH-tHS-tHW
geometric
IL_7A0S_093
IL_04638.4
IL_5DM8_0961/X/2652:2658,
1/X/2663:2668		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_7A0S_094
IL_16458.6
IL_5DM8_0971/X/2680:2684,
1/X/2725:2727		C-loop
geometric
IL_7A0S_095
IL_63596.13
IL_5DM8_0981/X/2687:2691,
1/X/2718:2722		UAA/GAN related, with intercalation
geometric
IL_7A0S_096
IL_82016.1
IL_5DM8_0991/X/2695:2696,
1/X/2711:2714		Multiple bulged bases
geometric
IL_7A0S_097
IL_44609.3
IL_5DM8_1001/X/2737:2742,
1/X/2762:2767		UAA/GAN with extra cWW
geometric
IL_7A0S_098
IL_91079.1
IL_5DM8_1011/X/2838:2839,
1/X/2878:2880		Major groove intercalation
geometric
IL_7A0S_099
IL_28408.3
IL_5DM8_1021/X/2843:2845,
1/X/2871:2874		Decoding loop related
geometric
IL_7A0S_100
IL_05502.1
IL_5DM8_1031/X/2847:2852,
1/X/2865:2869		No text annotation
geometric
IL_7A0S_101
IL_48489.2
IL_5DM8_1041/Y/19:21,
1/Y/66:69		Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010
IL_68118.5
IL_5DM8_1051/Y/25:30,
1/Y/58:62		No text annotation
homologous
IL_7A0S_103
IL_18472.5
IL_5DM8_1061/Y/32:33,
1/Y/53:56		No text annotation
IL_5DM8_1081/Y/73:81,
1/Y/100:108		Bacterial 5S Loop E
geometric
IL_7A0S_106
IL_71138.1
IL_5DM8_1091/Y/82:84,
1/Y/97:99		Isolated non-canonical cWW pair
geometric
IL_7A0S_107
IL_71625.4

Problematic loops

#loop idProblemSequence
IL_5DM8_003Major groove platform with extra cWW
IL_5DM8_022No text annotation
IL_5DM8_028No text annotation
IL_5DM8_031UAA/GAN with extra cWW
IL_5DM8_037No text annotation
IL_5DM8_047No text annotation
IL_5DM8_081No text annotation
IL_5DM8_082No text annotation
IL_5DM8_088Major groove platform with extra pair
IL_5DM8_107No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5DM8_0011/X/30:31,
1/X/474:481,
1/X/509:510		No text annotation
geometric
J3_7A0S_001
J3_68715.2
J3_5DM8_0031/X/683:689,
1/X/773:775,
1/X/791:794		No text annotation
geometric
J3_7A0S_004
J3_46658.2
J3_5DM8_0041/X/698:701,
1/X/731:736,
1/X/760:763		No text annotation
J3_5DM8_0051/X/1055:1058,
1/X/1080:1087,
1/X/1102:1104		No text annotation
J3_5DM8_0061/X/1298:1303,
1/X/1625:1626,
1/X/1639:1642		No text annotation
geometric
J3_7A0S_006
J3_32852.7
J3_5DM8_0071/X/1306:1309,
1/X/1605:1611,
1/X/1620:1622		No text annotation
geometric
J3_7A0S_007
J3_47341.1
J3_5DM8_0081/X/2091:2093,
1/X/2196:2200,
1/X/2223:2228		No text annotation
homologous
J3_7A0S_009
J3_17460.1
J3_5DM8_0091/X/2295:2297,
1/X/2321:2324,
1/X/2331:2337		No text annotation
J3_5DM8_0111/X/2789:2791,
1/X/2801:2811,
1/X/2889:2893		No text annotation
geometric
J3_7A0S_012
J3_20574.1
J3_5DM8_0121/X/2814:2815,
1/X/2831:2836,
1/X/2882:2886		No text annotation
geometric
J3_7A0S_013
J3_76911.2

Problematic loops

#loop idProblemSequence
J3_5DM8_002No text annotation
J3_5DM8_010No text annotation
J3_5DM8_013No text annotation

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