RNA 3D Hub //

6ZSC Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6ZSC_0011/AA/654:664No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_6ZSC_0041/AA/792:796No text annotation
geometric
HL_6U8D_003
HL_32346.6
HL_6ZSC_0051/AA/804:809No text annotation
HL_6ZSC_0071/AA/894:899GNRA
geometric
HL_1G1X_003
NA
HL_6ZSC_0081/AA/989:998No text annotation
geometric
HL_4LFB_015
HL_38491.2
HL_6ZSC_0091/AA/1023:1028GNRA
geometric
HL_4LFB_016
HL_34789.4
HL_6ZSC_0101/AA/1074:1084No text annotation
homologous
HL_5J7L_017
NA
HL_6ZSC_0121/AA/1150:1155No text annotation
geometric
HL_2Y9H_003
HL_75660.8
HL_6ZSC_0131/AA/1217:1226No text annotation
homologous
HL_5J7L_021
NA
HL_6ZSC_0141/AA/1281:1287No text annotation
geometric
HL_7RQB_011
NA
HL_6ZSC_0151/AA/1310:1315No text annotation
HL_6ZSC_0161/AA/1373:1379No text annotation
HL_6ZSC_0201/AA/1580:1585GNRA
homologous
HL_6CZR_103
NA
HL_6ZSC_0211/XA/1722:1729No text annotation
geometric
HL_4WF9_006
HL_48677.1
HL_6ZSC_0221/XA/1746:1752No text annotation
geometric
HL_5J7L_141
NA
HL_6ZSC_0231/XA/1786:1791GNRA
homologous
HL_4WF9_015
HL_34789.4
HL_6ZSC_0241/XA/1831:1839No text annotation
homologous
HL_7RQB_017
NA
HL_6ZSC_0251/XA/1847:1856T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_6ZSC_0261/XA/1884:1889No text annotation
geometric
HL_5TBW_006
NA
HL_6ZSC_0271/XA/1934:1940No text annotation
geometric
HL_1F1T_001
NA
HL_6ZSC_0281/XA/1954:1963No text annotation
homologous
HL_7RQB_023
NA
HL_6ZSC_0291/XA/1988:1996No text annotation
geometric
HL_5TBW_021
NA
HL_6ZSC_0301/XA/2035:2040No text annotation
homologous
HL_7RQB_025
NA
HL_6ZSC_0321/XA/2107:2114GNRA
homologous
HL_7RQB_027
NA
HL_6ZSC_0331/XA/2129:2136No text annotation
homologous
HL_5J7L_160
NA
HL_6ZSC_0341/XA/2175:2185No text annotation
homologous
HL_5J7L_161
NA
HL_6ZSC_0351/XA/2202:2209GNRA wlth tandem sheared
homologous
HL_6PRV_002
HL_98423.3
HL_6ZSC_0361/XA/2279:2286No text annotation
geometric
HL_2Y9H_005
HL_44506.2
HL_6ZSC_0371/XA/2319:2324UNCG
geometric
HL_4U7U_001
HL_61337.4
HL_6ZSC_0391/XA/2400:2403Mini UNCG
geometric
HL_5F9R_002
NA
HL_6ZSC_0401/XA/2428:2435No text annotation
homologous
HL_7RQB_040
NA
HL_6ZSC_0411/XA/2497:2507No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_6ZSC_0421/XA/2518:2532No text annotation
HL_6ZSC_0431/XA/2555:2560No text annotation
HL_6ZSC_0441/XA/2574:2583Externally structured
geometric
HL_8C3A_022
NA
HL_6ZSC_0451/XA/2612:2620No text annotation
homologous
HL_7A0S_048
HL_61418.2
HL_6ZSC_0461/XA/2690:2699No text annotation
homologous
HL_7RQB_050
NA
HL_6ZSC_0481/XA/2812:2820No text annotation
homologous
HL_4WF9_049
HL_11974.2
HL_6ZSC_0491/XA/2828:2840No text annotation
HL_6ZSC_0501/XA/2862:2870No text annotation
geometric
HL_2ZZM_002
HL_33487.1
HL_6ZSC_0511/XA/2902:2907GNRA
geometric
HL_6N2V_002
HL_34789.4
HL_6ZSC_0521/XA/2958:2966No text annotation
homologous
HL_4WF9_056
HL_52011.1
HL_6ZSC_0531/XA/3015:3022GNRA variation
homologous
HL_4WF9_057
HL_46665.2
HL_6ZSC_0541/XA/3037:3045No text annotation
HL_6ZSC_0551/XA/3081:3086GNRA
homologous
HL_7RQB_063
NA
HL_6ZSC_0561/XA/3126:3131GNRA related
geometric
HL_5J7L_179
NA
HL_6ZSC_0571/XA/3154:3159No text annotation
geometric
HL_5FMZ_001
HL_19413.2
HL_6ZSC_0581/XA/3176:3193No text annotation
geometric
HL_7A0S_074
NA
HL_6ZSC_0591/XA/3216:3224No text annotation
geometric
HL_5J7L_201
NA
HL_6ZSC_0611/XB/1630:1638tRNA anticodon loop
geometric
HL_4TUE_034
NA

Problematic loops

#loop idProblemSequence
HL_6ZSC_002No text annotation
HL_6ZSC_003GNRA
HL_6ZSC_006No text annotation
HL_6ZSC_011Externally structured
HL_6ZSC_017T-loop with 2 bulged bases not stacked
HL_6ZSC_018No text annotation
HL_6ZSC_019No text annotation
HL_6ZSC_031No text annotation
HL_6ZSC_038No text annotation
HL_6ZSC_047No text annotation
HL_6ZSC_060tRNA D-loop

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6ZSC_0011/AA/649:651,
1/AA/667:668		No text annotation
IL_6ZSC_0021/AA/674:676,
1/AA/921:923		Intercalated cWW
geometric
IL_7A0S_044
IL_53541.1
IL_6ZSC_0051/AA/694:696,
1/AA/819:820		Minor groove platform
homologous
IL_4LFB_004
IL_34520.3
IL_6ZSC_0061/AA/727:729,
1/AA/744:747		Minor groove platform with extra cWW
geometric
IL_7RQB_031
NA
IL_6ZSC_0081/AA/756:761,
1/AA/779:786		Kink-turn with non-sequential stacking
geometric
IL_6CZR_123
NA
IL_6ZSC_0091/AA/762:765,
1/AA/777:778		Major groove platform; stack outside cWW
geometric
IL_3DIL_004
IL_74641.2
IL_6ZSC_1011/AA/762:766,
1/AA/775:778		No text annotation
IL_6ZSC_0101/AA/765:766,
1/AA/775:777		No text annotation
IL_6ZSC_0111/AA/830:832,
1/AA/855:856		Single bulged U
geometric
IL_5J7L_017
NA
IL_6ZSC_0121/AA/834:838,
1/AA/852:853		C-loop
homologous
IL_5J7L_018
NA
IL_6ZSC_0131/AA/838:839,
1/AA/850:852		Single bulged A
geometric
IL_6WPI_001
IL_14190.2
IL_6ZSC_0141/AA/876:885,
1/AA/910:913		Tandem non-canonical cWW pairs
geometric
IL_5EW4_001
IL_76776.2
IL_6ZSC_0151/AA/887:893,
1/AA/900:908		Kink-turn related
geometric
IL_4V88_415
NA
IL_6ZSC_0161/AA/935:941,
1/AA/1133:1134		No text annotation
homologous
IL_5J7L_026
NA
IL_6ZSC_1031/AA/945:950,
1/AA/1044:1050		No text annotation
IL_6ZSC_0171/AA/946:950,
1/AA/1044:1049		No text annotation
IL_6ZSC_0181/AA/974:980,
1/AA/1008:1014		No text annotation
IL_6ZSC_0191/AA/982:984,
1/AA/1004:1006		Isolated non-canonical cWW pair
geometric
IL_4LFB_010
IL_01003.4
IL_6ZSC_0201/AA/986:988,
1/AA/999:1002		No text annotation
IL_6ZSC_0211/AA/1020:1022,
1/AA/1029:1030		Other IL
geometric
IL_3WBM_004
IL_18188.1
IL_6ZSC_0221/AA/1062:1066,
1/AA/1092:1093		Left turn
homologous
IL_5J7L_036
NA
IL_6ZSC_0231/AA/1067:1071,
1/AA/1087:1091		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_6ZSC_0241/AA/1109:1111,
1/AA/1130:1132		Isolated non-canonical cWW pair
geometric
IL_5MWI_004
IL_01003.4
IL_6ZSC_0251/AA/1139:1147,
1/AA/1158:1164		No text annotation
IL_6ZSC_1041/AA/1175:1176,
1/AA/1477:1479		Single bulged A
homologous
IL_6CZR_147
NA
IL_6ZSC_0271/AA/1178:1180,
1/AA/1474:1475		Single bulged G
homologous
IL_6CZR_148
NA
IL_6ZSC_1091/AA/1186:1190,
1/AA/1464:1468		C-loop
geometric
IL_8P9A_431
IL_63596.12
IL_6ZSC_0301/AA/1244:1252,
1/AA/1340:1345		No text annotation
IL_6ZSC_0311/AA/1253:1255,
1/AA/1338:1339		Single bulged U
homologous
IL_4LFB_042
IL_97561.5
IL_6ZSC_0351/AA/1266:1268,
1/AA/1323:1325		Isolated non-canonical cWW pair
homologous
IL_5J7L_050
NA
IL_6ZSC_0361/AA/1274:1277,
1/AA/1298:1301		Double sheared
geometric
IL_1SAQ_002
NA
IL_6ZSC_0371/AA/1278:1279,
1/AA/1289:1297		No text annotation
geometric
IL_8S95_001
IL_25652.1
IL_6ZSC_0391/AA/1483:1485,
1/AA/1566:1569		No text annotation
geometric
IL_5J7L_058
NA
IL_6ZSC_0401/AA/1485:1488,
1/AA/1562:1566		No text annotation
geometric
IL_4V88_464
NA
IL_6ZSC_0411/AA/1489:1491,
1/AA/1559:1561		Isolated non-canonical cWW pair
geometric
IL_5MWI_007
NA
IL_6ZSC_0421/AA/1491:1495,
1/AA/1554:1559		No text annotation
IL_6ZSC_0431/AA/1500:1504,
1/AA/1546:1549		UAA/GAN related
geometric
IL_2R8S_002
IL_77691.7
IL_6ZSC_0441/AA/1507:1510,
1/AA/1540:1543		Tandem non-canonical cWW pairs
geometric
IL_5TBW_128
NA
IL_6ZSC_0451/AA/1510:1511,
1/AA/1538:1540		No text annotation
IL_6ZSC_0461/AA/1511:1514,
1/AA/1535:1538		No text annotation
IL_6ZSC_0481/XA/1672:1678,
1/XA/1797:1816		No text annotation
IL_6ZSC_0491/XA/1682:1683,
1/XA/1768:1770		Single bulged A
homologous
IL_7A0S_002
IL_14190.2
IL_6ZSC_0501/XA/1739:1745,
1/XA/1753:1758		7x6 Sarcin-Ricin; G-bulge
geometric
IL_4V9F_106
IL_02666.1
IL_6ZSC_0511/XA/1845:1847,
1/XA/1856:1858		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_6ZSC_0521/XA/1877:1879,
1/XA/1895:1897		Isolated non-canonical cWW pair
geometric
IL_5MWI_007
NA
IL_6ZSC_0531/XA/1880:1883,
1/XA/1890:1894		No text annotation
IL_6ZSC_0541/XA/1904:1906,
1/XA/2016:2018		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.4
IL_6ZSC_0551/XA/1906:1910,
1/XA/2009:2016		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_6ZSC_0561/XA/1913:1915,
1/XA/2004:2006		Isolated non-canonical cWW pair
geometric
IL_5TBW_079
NA
IL_6ZSC_0571/XA/1925:1927,
1/XA/1977:1979		Isolated non-canonical cWW contact
geometric
IL_5UNE_001
IL_87720.1
IL_6ZSC_0581/XA/1929:1930,
1/XA/1973:1975		Single bulged A
homologous
IL_5J7L_261
NA
IL_6ZSC_0591/XA/1948:1951,
1/XA/1966:1968		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_6ZSC_0601/XA/1985:1987,
1/XA/1997:2001		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_6ZSC_0611/XA/2046:2048,
1/XA/2091:2094		No text annotation
geometric
IL_4N0T_004
IL_32983.2
IL_6ZSC_0621/XA/2057:2063,
1/XA/2076:2082		No text annotation
geometric
IL_5XWG_002
IL_74768.1
IL_6ZSC_0631/XA/2145:2147,
1/XA/2254:2255		Single bulged C
homologous
IL_5J7L_276
NA
IL_6ZSC_0641/XA/2149:2153,
1/XA/2248:2252		UAA/GAN
homologous
IL_7A0S_033
IL_08938.1
IL_6ZSC_0651/XA/2168:2173,
1/XA/2187:2192		No text annotation
IL_6ZSC_0661/XA/2197:2200,
1/XA/2211:2212		No text annotation
homologous
IL_6PRV_002
NA
IL_6ZSC_0671/XA/2306:2313,
1/XA/2674:2680		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6ZSC_1051/XA/2330:2333,
1/XA/2441:2447		No text annotation
IL_6ZSC_1061/XA/2377:2381,
1/XA/2411:2419		No text annotation
IL_6ZSC_1071/XA/2384:2400,
1/XA/2403:2408		No text annotation
IL_6ZSC_0691/XA/2456:2461,
1/XA/2666:2668		No text annotation
IL_6ZSC_0701/XA/2467:2469,
1/XA/2658:2660		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_6ZSC_0711/XA/2470:2473,
1/XA/2656:2657		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_6ZSC_1081/XA/2470:2478,
1/XA/2653:2657		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_6ZSC_0721/XA/2473:2478,
1/XA/2653:2656		Intercalated tWH
geometric
IL_5TBW_077
NA
IL_6ZSC_0731/XA/2478:2487,
1/XA/2648:2653		No text annotation
IL_6ZSC_0741/XA/2490:2491,
1/XA/2643:2645		Single bulged A
homologous
IL_7RQB_069
NA
IL_6ZSC_0751/XA/2548:2551,
1/XA/2566:2567		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_6ZSC_0761/XA/2552:2553,
1/XA/2562:2565		Major groove intercalation
homologous
IL_7A0S_067
IL_77710.1
IL_6ZSC_0771/XA/2596:2597,
1/XA/2627:2630		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_6ZSC_0781/XA/2597:2608,
1/XA/2624:2627		No text annotation
IL_6ZSC_0791/XA/2712:2715,
1/XA/3104:3106		No text annotation
geometric
IL_6DME_003
IL_75527.2
IL_6ZSC_0801/XA/2717:2719,
1/XA/3099:3102		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_6ZSC_0811/XA/2730:2732,
1/XA/2929:2930		Single bulged U
homologous
IL_7RQB_080
NA
IL_6ZSC_0821/XA/2733:2734,
1/XA/2925:2928		Minor groove platform
homologous
IL_7RQB_081
NA
IL_6ZSC_0831/XA/2744:2746,
1/XA/2802:2803		Minor groove platform
geometric
IL_7A0S_003
IL_34520.3
IL_6ZSC_0851/XA/2856:2860,
1/XA/2872:2876		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
NA
IL_6ZSC_0861/XA/2940:2941,
1/XA/2985:2987		Single stack bend
geometric
IL_7RQB_091
NA
IL_6ZSC_0871/XA/2941:2942,
1/XA/2983:2985		Major groove platform
homologous
IL_7RQB_092
NA
IL_6ZSC_0881/XA/2943:2946,
1/XA/2980:2982		Major groove platform with extra pair
geometric
IL_7RQB_093
NA
IL_6ZSC_0891/XA/2946:2948,
1/XA/2976:2980		Major groove minor groove platform with extra cWW
homologous
IL_7RQB_094
NA
IL_6ZSC_0901/XA/2953:2955,
1/XA/2968:2971		No text annotation
geometric
IL_4P3T_002
NA
IL_6ZSC_0911/XA/2955:2957,
1/XA/2967:2968		Minor groove platform
geometric
IL_4V88_412
NA
IL_6ZSC_0921/XA/2994:2995,
1/XA/3067:3069		Major groove platform
homologous
IL_7RQB_096
NA
IL_6ZSC_0931/XA/2997:2999,
1/XA/3061:3065		Isolated non-canonical cWW with bulges
homologous
IL_4WF9_095
IL_68118.4
IL_6ZSC_0941/XA/2999:3000,
1/XA/3058:3061		No text annotation
geometric
IL_4WF9_096
IL_44609.2
IL_6ZSC_0951/XA/3008:3010,
1/XA/3027:3031		No text annotation
IL_6ZSC_0961/XA/3078:3079,
1/XA/3088:3090		Single bulged A
homologous
IL_7RQB_101
NA
IL_6ZSC_0971/XA/3115:3117,
1/XA/3139:3141		Isolated non-canonical cWW pair
geometric
IL_4LFB_061
NA
IL_6ZSC_0981/XA/3119:3126,
1/XA/3131:3137		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_6ZSC_0991/XA/3148:3152,
1/XA/3161:3163		C-loop
geometric
IL_6JDV_004
IL_63596.12
IL_6ZSC_1001/XB/1627:1629,
1/XB/1639:1641		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.4

Problematic loops

#loop idProblemSequence
IL_6ZSC_003Single stack bend
IL_6ZSC_004Single bulged A
IL_6ZSC_007No text annotation
IL_6ZSC_102Single bulged G, near cWW
IL_6ZSC_026Isolated non-canonical cWW with bulges
IL_6ZSC_028No text annotation
IL_6ZSC_029No text annotation
IL_6ZSC_110Multiple bulged bases
IL_6ZSC_032Isolated cWS basepair
IL_6ZSC_033Minor groove platform
IL_6ZSC_034Single bulged A
IL_6ZSC_038No text annotation
IL_6ZSC_047No text annotation
IL_6ZSC_068No text annotation
IL_6ZSC_084No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6ZSC_0021/AA/687:692,
1/AA/822:830,
1/AA/856:858		No text annotation
homologous
J3_5J7L_050
NA
J3_6ZSC_0031/AA/973:974,
1/AA/1014:1020,
1/AA/1030:1031		No text annotation
J3_6ZSC_0041/AA/1192:1194,
1/AA/1428:1434,
1/AA/1456:1462		No text annotation
J3_6ZSC_0051/AA/1198:1201,
1/AA/1364:1366,
1/AA/1421:1424		No text annotation
homologous
J3_6CZR_019
NA
J3_6ZSC_0061/AA/1210:1216,
1/AA/1227:1238,
1/AA/1351:1354		No text annotation
J3_6ZSC_0171/AA/1268:1273,
1/AA/1302:1308,
1/AA/1317:1323		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J3_6ZSC_0091/XA/1678:1681,
1/XA/1771:1785,
1/XA/1792:1797		No text annotation
J3_6ZSC_0151/XA/1684:1722,
1/XA/1729:1739,
1/XA/1758:1767		No text annotation
J3_6ZSC_0101/XA/1915:1921,
1/XA/1983:1985,
1/XA/2001:2004		No text annotation
homologous
J3_5J7L_038
NA
J3_6ZSC_0111/XA/1930:1932,
1/XA/1942:1946,
1/XA/1970:1973		No text annotation
homologous
J3_7RQB_005
NA
J3_6ZSC_0121/XA/2336:2343,
1/XA/2423:2427,
1/XA/2436:2438		No text annotation
J3_6ZSC_0131/XA/2343:2345,
1/XA/2368:2375,
1/XA/2421:2423		No text annotation
J3_6ZSC_0161/XA/2846:2848,
1/XA/2890:2900,
1/XA/2909:2915		No text annotation
J3_6ZSC_0141/XA/3004:3007,
1/XA/3032:3034,
1/XA/3048:3054		No text annotation
homologous
J3_7RQB_012
NA
J4_6ZSC_0011/AA/698:701,
1/AA/708:715,
1/AA/800:802,
1/AA/811:817		No text annotation
J4_6ZSC_0021/AA/717:725,
1/AA/749:753,
1/AA/789:791,
1/AA/797:798		No text annotation
J4_6ZSC_0031/AA/941:943,
1/AA/1052:1057,
1/AA/1098:1109,
1/AA/1132:1133		No text annotation
homologous
J4_5J7L_003
NA
J4_6ZSC_0041/XA/2314:2317,
1/XA/2326:2327,
1/XA/2450:2453,
1/XA/2671:2673		No text annotation
J4_6ZSC_0051/XA/2336:2345,
1/XA/2368:2375,
1/XA/2421:2427,
1/XA/2436:2438		No text annotation
J4_6ZSC_0061/XA/2492:2496,
1/XA/2508:2513,
1/XA/2537:2542,
1/XA/2637:2642		No text annotation
J4_6ZSC_0071/XA/2544:2546,
1/XA/2569:2570,
1/XA/2587:2596,
1/XA/2630:2635		No text annotation
homologous
J4_5J7L_026
NA
J5_6ZSC_0011/XA/1827:1829,
1/XA/1841:1845,
1/XA/1858:1860,
1/XA/2305:2306,
1/XA/2680:2681		No text annotation
homologous
J5_7A0S_003
J5_43153.6
J5_6ZSC_0021/XA/1865:1875,
1/XA/1899:1903,
1/XA/2019:2022,
1/XA/2271:2275,
1/XA/2290:2300		No text annotation
J5_6ZSC_0031/XA/2720:2727,
1/XA/2933:2940,
1/XA/2987:2993,
1/XA/3070:3075,
1/XA/3093:3098		No text annotation
J5_6ZSC_0041/XA/2737:2740,
1/XA/2807:2810,
1/XA/2822:2823,
1/XA/2845:2846,
1/XA/2915:2922		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_6ZSC_0011/XA/2027:2032,
1/XA/2043:2046,
1/XA/2094:2098,
1/XA/2123:2127,
1/XA/2138:2143,
1/XA/2257:2266		No text annotation
J6_6ZSC_0021/XA/2737:2740,
1/XA/2807:2810,
1/XA/2822:2823,
1/XA/2845:2848,
1/XA/2890:2900,
1/XA/2909:2922		No text annotation

Problematic loops

#loop idProblemSequence
J3_6ZSC_001No text annotation
J3_6ZSC_007No text annotation
J3_6ZSC_008No text annotation

Coloring options:
Copyright 2026 BGSU RNA group. Page generated in 0.0541 s