RNA 3D Hub //

4KZZ Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4KZZ_0011/i/7:17No text annotation
homologous
HL_4V88_186
NA
HL_4KZZ_0021/i/69:80No text annotation
HL_4KZZ_0031/i/156:162GNRA related
homologous
HL_4V88_188
NA
HL_4KZZ_0041/i/194:201No text annotation
geometric
HL_2Y9H_005
HL_45127.1
HL_4KZZ_0061/i/279:286T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_4KZZ_0071/i/312:319No text annotation
geometric
HL_5TBW_012
NA
HL_4KZZ_0081/i/367:377No text annotation
geometric
HL_3SKL_006
NA
HL_4KZZ_0091/i/406:411No text annotation
homologous
HL_4V88_194
NA
HL_4KZZ_0101/i/431:442No text annotation
homologous
HL_4V88_195
NA
HL_4KZZ_0111/i/452:457UNCG
homologous
HL_4V88_196
NA
HL_4KZZ_0121/i/488:494No text annotation
homologous
HL_4V88_197
NA
HL_4KZZ_0131/i/529:534GNRA
geometric
HL_4FRG_002
HL_37824.3
HL_4KZZ_0141/i/559:571No text annotation
geometric
HL_4V88_199
NA
HL_4KZZ_0151/i/608:613GNRA variation
homologous
HL_4V88_200
NA
HL_4KZZ_0171/i/816:824No text annotation
homologous
HL_4V88_203
NA
HL_4KZZ_0181/i/829:837No text annotation
homologous
HL_8P9A_207
HL_48417.2
HL_4KZZ_0191/i/881:897Pseudoknot geometry
homologous
HL_4V88_205
NA
HL_4KZZ_0201/i/953:962No text annotation
homologous
HL_4V88_206
NA
HL_4KZZ_0211/i/990:995GNRA
homologous
HL_4V88_207
NA
HL_4KZZ_0221/i/1050:1060No text annotation
homologous
HL_4V88_208
NA
HL_4KZZ_0231/i/1108:1117No text annotation
HL_4KZZ_0251/i/1174:1179GNRA
homologous
HL_4V88_211
NA
HL_4KZZ_0261/i/1241:1250No text annotation
homologous
HL_4V88_212
NA
HL_4KZZ_0271/i/1291:1300Anticodon loop related
homologous
HL_4V88_213
NA
HL_4KZZ_0291/i/1362:1369No text annotation
homologous
HL_4V88_215
NA
HL_4KZZ_0301/i/1417:1422GNRA
geometric
HL_3SUX_002
HL_37824.3
HL_4KZZ_0311/i/1456:1462GNRA
homologous
HL_4V88_217
NA
HL_4KZZ_0321/i/1560:1565GNRA
homologous
HL_4V88_218
NA
HL_4KZZ_0331/i/1609:1620No text annotation
homologous
HL_4V88_219
NA
HL_4KZZ_0391/i/1755:1765No text annotation
HL_4KZZ_0351/i/1841:1846GNRA variation
homologous
HL_4V88_222
NA
HL_4KZZ_0361/j/13:21tRNA D-loop
homologous
HL_5B63_003
HL_20811.2
HL_4KZZ_0381/j/52:60T-loop with 2 stacked bulged bases
homologous
HL_5AH5_008
HL_28252.2

Problematic loops

#loop idProblemSequence
HL_4KZZ_005No text annotation
HL_4KZZ_016No text annotation
HL_4KZZ_024GNRA
HL_4KZZ_028GNRA
HL_4KZZ_034No text annotation
HL_4KZZ_037tRNA anticodon loop

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4KZZ_0011/i/23:25,
1/i/639:641		Isolated non-canonical cWW pair
geometric
IL_5TBW_021
NA
IL_4KZZ_0031/i/37:40,
1/i/504:508		Double sheared
geometric
IL_4WF9_016
IL_09705.13
IL_4KZZ_0041/i/41:47,
1/i/469:471		No text annotation
homologous
IL_4V88_387
NA
IL_4KZZ_0061/i/57:62,
1/i/86:88		No text annotation
homologous
IL_4V88_389
NA
IL_4KZZ_0071/i/63:68,
1/i/81:85		No text annotation
homologous
IL_4V88_390
NA
IL_4KZZ_0081/i/108:110,
1/i/341:343		Isolated non-canonical cWW pair
geometric
IL_1ZX7_004
NA
IL_4KZZ_0101/i/112:115,
1/i/338:339		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_4KZZ_0111/i/116:121,
1/i/333:337		No text annotation
homologous
IL_4V88_393
NA
IL_4KZZ_0121/i/145:151,
1/i/167:174		tWH-tWH-tHW-tHW
homologous
IL_4V88_394
NA
IL_4KZZ_0131/i/152:154,
1/i/164:166		No text annotation
geometric
IL_2ZNI_001
NA
IL_4KZZ_0141/i/186:191,
1/i/204:209		Double sheared; A in syn; two near cWW pairs
geometric
IL_4N0T_001
IL_71294.3
IL_4KZZ_1101/i/187:194,
1/i/201:208		No text annotation
IL_4KZZ_0151/i/192:194,
1/i/201:203		Isolated non-canonical cWW pair
geometric
IL_1ZZ5_002
NA
IL_4KZZ_0161/i/213:216,
1/i/293:300		No text annotation
geometric
IL_1GID_008
IL_68538.1
IL_4KZZ_0181/i/237:239,
1/i/271:272		No text annotation
IL_4KZZ_0191/i/303:305,
1/i/326:327		No text annotation
IL_4KZZ_0211/i/308:310,
1/i/321:323		Isolated non-canonical cWW pair
geometric
IL_7A0S_038
IL_37047.1
IL_4KZZ_0221/i/349:354,
1/i/386:393		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_4KZZ_0231/i/356:361,
1/i/383:384		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_4KZZ_0241/i/401:403,
1/i/414:419		No text annotation
homologous
IL_4V88_404
NA
IL_4KZZ_0251/i/427:429,
1/i/444:446		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_4KZZ_0261/i/449:451,
1/i/458:460		Isolated near basepair
homologous
IL_4V88_406
NA
IL_4KZZ_0271/i/477:479,
1/i/501:502		Single bulged U
homologous
IL_4V88_407
NA
IL_4KZZ_1281/i/481:485,
1/i/498:499		No text annotation
IL_4KZZ_1291/i/485:486,
1/i/496:498		No text annotation
IL_4KZZ_0291/i/519:521,
1/i/543:546		No text annotation
IL_4KZZ_0301/i/524:525,
1/i/538:540		Single stack bend
geometric
IL_5J7L_044
IL_06586.1
IL_4KZZ_0311/i/525:527,
1/i/536:538		No text annotation
geometric
IL_4WF9_055
NA
IL_4KZZ_0321/i/556:559,
1/i/571:574		Double sheared
geometric
IL_4LFB_060
IL_09705.13
IL_4KZZ_1301/i/589:598,
1/i/625:627		No text annotation
IL_4KZZ_0341/i/601:607,
1/i/614:622		Kink-turn related
homologous
IL_4V88_415
NA
IL_4KZZ_0351/i/653:655,
1/i/1158:1160		Isolated non-canonical cWW pair
geometric
IL_4KNQ_003
IL_10289.1
IL_4KZZ_0361/i/655:661,
1/i/1157:1158		No text annotation
geometric
IL_4V88_416
NA
IL_4KZZ_0371/i/663:665,
1/i/1026:1028		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_4KZZ_0381/i/666:670,
1/i/1021:1025		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_4KZZ_0411/i/687:691,
1/i/725:729		No text annotation
geometric
IL_5TBW_121
NA
IL_4KZZ_0421/i/741:743,
1/i/790:792		Isolated non-canonical cWW pair
geometric
IL_5TBW_079
NA
IL_4KZZ_0431/i/798:799,
1/i/856:859		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_4KZZ_0441/i/800:803,
1/i/852:855		Tandem non-canonical cWW pairs
geometric
IL_7A0S_040
IL_54697.2
IL_4KZZ_1311/i/803:811,
1/i/845:852		No text annotation
IL_4KZZ_0461/i/870:872,
1/i/906:907		Single stack bend
geometric
IL_7KGA_003
NA
IL_4KZZ_0471/i/872:875,
1/i/903:906		No text annotation
IL_4KZZ_1321/i/918:919,
1/i/1015:1018		No text annotation
IL_4KZZ_1151/i/921:922,
1/i/1011:1013		Single bulged U
geometric
IL_3NDB_005
IL_89505.1
IL_4KZZ_0511/i/924:927,
1/i/1006:1009		Tandem non-canonical cWW pairs
geometric
IL_4V88_430
NA
IL_4KZZ_0521/i/927:931,
1/i/1003:1006		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_4KZZ_0531/i/938:941,
1/i/977:980		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_4KZZ_0541/i/948:952,
1/i/963:970		Kink-turn
homologous
IL_4V88_434
NA
IL_4KZZ_0561/i/1038:1043,
1/i/1067:1069		Other IL
geometric
IL_4V88_435
NA
IL_4KZZ_0571/i/1043:1047,
1/i/1063:1067		tSH-tHW-tHS
homologous
IL_4V88_436
NA
IL_4KZZ_1161/i/1087:1089,
1/i/1148:1154		No text annotation
homologous
IL_8P9A_425
IL_47729.1
IL_4KZZ_0591/i/1094:1097,
1/i/1127:1130		Tandem non-canonical cWW pairs
geometric
IL_4V88_438
NA
IL_4KZZ_0601/i/1097:1099,
1/i/1125:1127		Isolated non-canonical cWW pair
geometric
IL_1RPU_001
IL_10289.1
IL_4KZZ_0611/i/1104:1106,
1/i/1119:1120		Single bulged C
geometric
IL_4WF9_035
IL_61258.14
IL_4KZZ_0631/i/1164:1171,
1/i/1182:1187		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_4KZZ_0651/i/1202:1204,
1/i/1686:1687		Single bulged G
homologous
IL_4V88_442
NA
IL_4KZZ_1171/i/1210:1213,
1/i/1676:1680		C-loop
homologous
IL_8C3A_449
IL_63596.10
IL_4KZZ_0671/i/1226:1228,
1/i/1521:1523		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_4KZZ_1181/i/1231:1232,
1/i/1516:1518		No text annotation
homologous
IL_8C3A_451
IL_92540.1
IL_4KZZ_0691/i/1266:1268,
1/i/1506:1507		Single stack bend
geometric
IL_7A0S_022
IL_68541.2
IL_4KZZ_0701/i/1277:1283,
1/i/1310:1312		No text annotation
IL_4KZZ_1191/i/1277:1286,
1/i/1305:1312		No text annotation
IL_4KZZ_0711/i/1283:1286,
1/i/1305:1310		No text annotation
IL_4KZZ_0721/i/1287:1289,
1/i/1302:1304		No text annotation
homologous
IL_4V88_448
NA
IL_4KZZ_0731/i/1321:1323,
1/i/1498:1499		Single bulged U
homologous
IL_4V88_449
NA
IL_4KZZ_1201/i/1325:1331,
1/i/1488:1496		No text annotation
geometric
IL_4V88_510
NA
IL_4KZZ_1211/i/1329:1331,
1/i/1488:1494		No text annotation
homologous
IL_8P9A_440
IL_97255.2
IL_4KZZ_0761/i/1330:1331,
1/i/1488:1492		Minor groove platform
geometric
IL_5J7L_048
IL_58310.1
IL_4KZZ_0781/i/1343:1345,
1/i/1376:1378		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_4KZZ_0791/i/1359:1361,
1/i/1370:1371		Minor groove platform
geometric
IL_5ML7_009
IL_92540.1
IL_4KZZ_1221/i/1398:1401,
1/i/1437:1440		No text annotation
homologous
IL_8C3A_462
IL_25234.1
IL_4KZZ_0821/i/1404:1407,
1/i/1431:1434		No text annotation
IL_4KZZ_0831/i/1407:1409,
1/i/1429:1431		No text annotation
IL_4KZZ_0841/i/1411:1413,
1/i/1425:1427		No text annotation
IL_4KZZ_0851/i/1413:1415,
1/i/1424:1425		Major groove platform
geometric
IL_5Y85_005
IL_48076.2
IL_4KZZ_0861/i/1449:1452,
1/i/1466:1471		No text annotation
IL_4KZZ_1231/i/1532:1534,
1/i/1589:1591		Isolated non-canonical cWW pair
geometric
IL_4KNQ_003
IL_10289.1
IL_4KZZ_1241/i/1536:1553,
1/i/1572:1587		No text annotation
IL_4KZZ_0881/i/1545:1553,
1/i/1572:1577		180 degree turn
geometric
IL_6CZR_161
IL_11344.1
IL_4KZZ_0891/i/1555:1557,
1/i/1568:1570		Isolated non-canonical cWW
geometric
IL_7A0S_107
IL_10289.1
IL_4KZZ_0911/i/1599:1605,
1/i/1624:1630		No text annotation
homologous
IL_8C3A_469
NA
IL_4KZZ_0921/i/1695:1697,
1/i/1827:1830		No text annotation
geometric
IL_4V88_463
NA
IL_4KZZ_0931/i/1697:1700,
1/i/1823:1827		No text annotation
homologous
IL_4V88_464
NA
IL_4KZZ_0941/i/1701:1703,
1/i/1820:1822		Isolated non-canonical cWW pair
geometric
IL_4V88_465
NA
IL_4KZZ_0951/i/1703:1706,
1/i/1816:1820		No text annotation
geometric
IL_6AZ4_001
NA
IL_4KZZ_0961/i/1709:1711,
1/i/1811:1813		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_4KZZ_0971/i/1712:1715,
1/i/1807:1810		Double sheared
geometric
IL_4V88_468
NA
IL_4KZZ_0981/i/1715:1717,
1/i/1806:1807		No text annotation
IL_4KZZ_1251/i/1724:1726,
1/i/1797:1799		Isolated non-canonical cWW
homologous
IL_8C3A_477
IL_10289.1
IL_4KZZ_1001/i/1728:1731,
1/i/1792:1795		Double sheared
geometric
IL_4V88_471
NA
IL_4KZZ_1021/i/1734:1737,
1/i/1786:1789		Tandem non-canonical cWW pairs
geometric
IL_4V88_473
NA
IL_4KZZ_1031/i/1737:1741,
1/i/1782:1786		Triple sheared
homologous
IL_4V88_474
NA
IL_4KZZ_1051/i/1745:1747,
1/i/1774:1778		Other IL
geometric
IL_5TBW_064
NA
IL_4KZZ_1271/i/1747:1748,
1/i/1772:1774		Intercalated cWW
geometric
IL_4WF9_047
IL_31737.2

Problematic loops

#loop idProblemSequence
IL_4KZZ_002Isolated non-canonical cWW pair
IL_4KZZ_005Minor groove platform
IL_4KZZ_009Isolated non-canonical cWW pair
IL_4KZZ_017No text annotation
IL_4KZZ_020Self complementary
IL_4KZZ_111No text annotation
IL_4KZZ_028C-loop with extra cWW pair
IL_4KZZ_112No text annotation
IL_4KZZ_033No text annotation
IL_4KZZ_039No text annotation
IL_4KZZ_113Triple non-canonical cWW pairs
IL_4KZZ_040No text annotation
IL_4KZZ_114No text annotation
IL_4KZZ_045No text annotation
IL_4KZZ_048Isolated cWH basepair
IL_4KZZ_049Isolated cWH basepair
IL_4KZZ_050Tandem non-canonical cWW pairs
IL_4KZZ_055Isolated non-canonical cWW pair
IL_4KZZ_058No text annotation
IL_4KZZ_062Isolated non-canonical cWW pair
IL_4KZZ_064Single bulged A
IL_4KZZ_066C-loop with extra cWW pair
IL_4KZZ_068Isolated non-canonical cWW with bulges
IL_4KZZ_074Isolated cWS basepair
IL_4KZZ_075No text annotation
IL_4KZZ_077Single bulged A
IL_4KZZ_080Tandem non-canonical cWW pairs
IL_4KZZ_081No text annotation
IL_4KZZ_087No text annotation
IL_4KZZ_090Isolated non-canonical cWW pair
IL_4KZZ_099Tandem non-canonical cWW pairs
IL_4KZZ_101Isolated non-canonical cWW pair
IL_4KZZ_104No text annotation
IL_4KZZ_126No text annotation
IL_4KZZ_106No text annotation
IL_4KZZ_107Tandem non-canonical cWW pairs
IL_4KZZ_108No text annotation
IL_4KZZ_109Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4KZZ_0111/i/40:41,
1/i/471:477,
1/i/502:504		No text annotation
geometric
J3_4V88_078
NA
J3_4KZZ_0131/i/40:47,
1/i/469:477,
1/i/502:504		No text annotation
homologous
J3_8P9A_069
NA
J3_4KZZ_0141/i/220:235,
1/i/274:279,
1/i/286:289		No text annotation
J3_4KZZ_0191/i/672:674,
1/i/914:918,
1/i/1018:1019		No text annotation
J3_4KZZ_0011/i/672:674,
1/i/914:919,
1/i/1015:1019		No text annotation
homologous
J3_8C3A_034
NA
J3_4KZZ_0151/i/812:815,
1/i/825:827,
1/i/839:844		No text annotation
homologous
J3_8P9A_073
NA
J3_4KZZ_0021/i/934:937,
1/i/981:989,
1/i/996:1000		No text annotation
homologous
J3_4V88_033
NA
J3_4KZZ_0161/i/1090:1092,
1/i/1132:1136,
1/i/1143:1147		No text annotation
J3_4KZZ_0041/i/1214:1217,
1/i/1640:1646,
1/i/1668:1675		No text annotation
homologous
J3_4V88_035
NA
J3_4KZZ_0051/i/1221:1224,
1/i/1525:1527,
1/i/1633:1636		No text annotation
homologous
J3_4V88_036
NA
J3_4KZZ_0061/i/1233:1240,
1/i/1251:1262,
1/i/1511:1515		No text annotation
homologous
J3_8P9A_078
NA
J3_4KZZ_0071/i/1268:1273,
1/i/1316:1320,
1/i/1500:1506		No text annotation
homologous
J3_8C3A_041
NA
J3_4KZZ_0081/i/1336:1341,
1/i/1380:1385,
1/i/1477:1482		No text annotation
J3_4KZZ_0121/i/1346:1347,
1/i/1356:1359,
1/i/1371:1375		No text annotation
homologous
J3_8C3A_085
NA
J3_4KZZ_0091/i/1387:1391,
1/i/1446:1449,
1/i/1471:1475		No text annotation
J3_4KZZ_0181/i/1387:1391,
1/i/1446:1452,
1/i/1466:1475		No text annotation
J3_4KZZ_0101/i/1527:1531,
1/i/1592:1599,
1/i/1630:1633		No text annotation
homologous
J3_4V88_041
NA
J4_4KZZ_0011/i/98:106,
1/i/345:347,
1/i/395:399,
1/i/421:422		No text annotation
homologous
J4_8C3A_021
NA
J4_4KZZ_0021/i/661:663,
1/i/1028:1033,
1/i/1074:1085,
1/i/1156:1157		No text annotation
homologous
J4_8P9A_022
NA
J4_4KZZ_0031/j/7:10,
1/j/24:26,
1/j/42:48,
1/j/64:65		No text annotation
homologous
J4_4TUE_004
NA
J5_4KZZ_0011/i/30:34,
1/i/511:517,
1/i/548:555,
1/i/575:585,
1/i/631:634		No text annotation
J5_4KZZ_0021/i/53:56,
1/i/89:96,
1/i/424:426,
1/i/447:449,
1/i/460:464		No text annotation
homologous
J5_8C3A_020
NA
J5_4KZZ_0031/i/123:144,
1/i/175:186,
1/i/209:212,
1/i/301:303,
1/i/327:331		No text annotation
J5_4KZZ_0041/i/123:144,
1/i/175:186,
1/i/209:212,
1/i/301:305,
1/i/326:331		No text annotation

Problematic loops

#loop idProblemSequence
J3_4KZZ_003No text annotation
J3_4KZZ_017No text annotation

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