RNA 3D Hub //

8PJ4 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8PJ4_0011/A/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_8PJ4_0021/A/69:80No text annotation
HL_8PJ4_0031/A/156:162GNRA related
homologous
HL_8C3A_194
NA
HL_8PJ4_0051/A/288:295T-loop with 1 bulged base
geometric
HL_4V88_191
NA
HL_8PJ4_0071/A/377:387tRNA D-loop
geometric
HL_5AXM_001
HL_20490.1
HL_8PJ4_0081/A/416:421GNRA variation
homologous
HL_8C3A_200
NA
HL_8PJ4_0091/A/441:452No text annotation
homologous
HL_8C3A_201
NA
HL_8PJ4_0101/A/462:467UNCG
homologous
HL_8C3A_202
NA
HL_8PJ4_0111/A/498:504No text annotation
homologous
HL_8C3A_203
NA
HL_8PJ4_0131/A/569:581No text annotation
homologous
HL_8C3A_205
NA
HL_8PJ4_0141/A/618:623GNRA variation
homologous
HL_8C3A_206
NA
HL_8PJ4_0171/A/820:828No text annotation
homologous
HL_8C3A_208
NA
HL_8PJ4_0181/A/833:841No text annotation
HL_8PJ4_0201/A/957:966No text annotation
homologous
HL_8C3A_211
NA
HL_8PJ4_0211/A/994:999GNRA
homologous
HL_8C3A_212
NA
HL_8PJ4_0221/A/1054:1064No text annotation
homologous
HL_4V88_208
NA
HL_8PJ4_0401/A/1112:1121No text annotation
HL_8PJ4_0241/A/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_8PJ4_0251/A/1178:1183GNRA
homologous
HL_8C3A_216
NA
HL_8PJ4_0261/A/1245:1254No text annotation
homologous
HL_8C3A_217
NA
HL_8PJ4_0271/A/1295:1304Anticodon loop related
homologous
HL_8C3A_218
NA
HL_8PJ4_0281/A/1353:1358GNRA
homologous
HL_8C3A_219
NA
HL_8PJ4_0291/A/1366:1373T-loop related
homologous
HL_8C3A_220
NA
HL_8PJ4_0301/A/1416:1424No text annotation
geometric
HL_361D_002
NA
HL_8PJ4_0311/A/1460:1466No text annotation
homologous
HL_8C3A_222
NA
HL_8PJ4_0321/A/1565:1570GNRA
homologous
HL_8C3A_223
NA
HL_8PJ4_0331/A/1614:1625No text annotation
homologous
HL_8C3A_224
NA
HL_8PJ4_0341/A/1658:1666No text annotation
homologous
HL_8C3A_225
NA
HL_8PJ4_0361/A/1847:1852GNRA variation
homologous
HL_8C3A_227
NA
HL_8PJ4_0381/w/31:39tRNA anticodon loop
homologous
HL_4TUE_034
NA

Problematic loops

#loop idProblemSequence
HL_8PJ4_004No text annotation
HL_8PJ4_006No text annotation
HL_8PJ4_012Externally structured
HL_8PJ4_015GNRA
HL_8PJ4_016No text annotation
HL_8PJ4_019No text annotation
HL_8PJ4_023No text annotation
HL_8PJ4_035No text annotation
HL_8PJ4_037tRNA D-loop
HL_8PJ4_039T-loop with 2 stacked bulged bases

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8PJ4_0011/A/23:25,
1/A/649:651		Isolated non-canonical cWW pair
geometric
IL_1U9S_007
IL_01003.4
IL_8PJ4_0031/A/34:36,
1/A/519:521		Isolated non-canonical cWW pair
homologous
IL_8C3A_393
NA
IL_8PJ4_0041/A/37:40,
1/A/514:518		Double sheared
geometric
IL_4WF9_016
IL_58355.2
IL_8PJ4_0051/A/41:47,
1/A/479:481		No text annotation
homologous
IL_4V88_387
NA
IL_8PJ4_0061/A/49:51,
1/A/476:477		Minor groove platform
homologous
IL_8C3A_396
NA
IL_8PJ4_0071/A/57:62,
1/A/86:88		No text annotation
homologous
IL_4V88_389
NA
IL_8PJ4_0081/A/63:68,
1/A/81:85		No text annotation
homologous
IL_4V88_390
NA
IL_8PJ4_0091/A/108:110,
1/A/351:353		Isolated non-canonical cWW pair
geometric
IL_1ZX7_006
IL_71625.3
IL_8PJ4_0991/A/108:112,
1/A/349:353		Triple non-canonical cWW pairs
geometric
IL_8VMB_003
IL_71154.3
IL_8PJ4_0101/A/110:112,
1/A/349:351		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_01003.4
IL_8PJ4_0111/A/112:115,
1/A/348:349		Multiple bulged bases
geometric
IL_4V88_392
NA
IL_8PJ4_1001/A/116:121,
1/A/343:347		No text annotation
homologous
IL_8C3A_401
NA
IL_8PJ4_0131/A/123:124,
1/A/339:341		Minor groove platform
geometric
IL_4V88_388
NA
IL_8PJ4_1011/A/145:151,
1/A/167:174		No text annotation
homologous
IL_8C3A_402
NA
IL_8PJ4_1021/A/152:154,
1/A/164:166		No text annotation
homologous
IL_8P9A_384
IL_87720.1
IL_8PJ4_0171/A/188:192,
1/A/207:211		Double sheared with non-canonical cWW
geometric
IL_4WFL_001
IL_87767.2
IL_8PJ4_0181/A/216:219,
1/A/302:309		Tandem non-canonical cWW pairs
geometric
IL_1GID_008
NA
IL_8PJ4_0201/A/312:314,
1/A/336:337		Single bulged A
homologous
IL_4V88_399
NA
IL_8PJ4_0211/A/317:319,
1/A/332:333		No text annotation
IL_8PJ4_0221/A/359:364,
1/A/396:403		Kink-turn with non-sequential stacking
homologous
IL_8C3A_410
NA
IL_8PJ4_0231/A/366:371,
1/A/393:394		No text annotation
geometric
IL_5Y58_001
IL_37738.1
IL_8PJ4_0241/A/411:413,
1/A/424:429		No text annotation
homologous
IL_8C3A_412
NA
IL_8PJ4_0251/A/437:439,
1/A/454:456		Isolated cWH basepair
homologous
IL_8C3A_413
NA
IL_8PJ4_0261/A/459:461,
1/A/468:470		Isolated non-canonical cWW pair
homologous
IL_8C3A_414
NA
IL_8PJ4_0271/A/487:489,
1/A/511:512		Single bulged U
homologous
IL_4V88_407
NA
IL_8PJ4_0281/A/490:495,
1/A/508:510		No text annotation
IL_8PJ4_0291/A/495:496,
1/A/506:508		Single bulged G
homologous
IL_8C3A_417
NA
IL_8PJ4_0301/A/527:534,
1/A/549:558		No text annotation
IL_8PJ4_0311/A/535:537,
1/A/546:548		Multiple bulged bases
geometric
IL_5W1H_001
IL_71421.2
IL_8PJ4_0321/A/563:565,
1/A/585:592		No text annotation
homologous
IL_8C3A_420
NA
IL_8PJ4_0331/A/566:569,
1/A/581:584		Tandem non-canonical cWW pairs
geometric
IL_6JDV_001
IL_71194.2
IL_8PJ4_0341/A/599:606,
1/A/636:637		SSU/LSU pseudoknot
homologous
IL_8C3A_423
NA
IL_8PJ4_0351/A/606:608,
1/A/635:636		Single bulged U
geometric
IL_4V88_407
NA
IL_8PJ4_0361/A/611:617,
1/A/624:632		Kink-turn related
homologous
IL_4V88_415
NA
IL_8PJ4_0371/A/663:665,
1/A/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_01003.4
IL_8PJ4_0381/A/665:671,
1/A/1161:1162		No text annotation
homologous
IL_8C3A_426
NA
IL_8PJ4_0391/A/673:675,
1/A/1030:1032		Isolated non-canonical cWW pair
homologous
IL_8C3A_427
NA
IL_8PJ4_0401/A/676:680,
1/A/1025:1029		tSH-tHW-tHS
homologous
IL_8C3A_428
NA
IL_8PJ4_0441/A/802:803,
1/A/860:863		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_8PJ4_0451/A/805:807,
1/A/856:858		Isolated non-canonical cWW pair
homologous
IL_8C3A_431
NA
IL_8PJ4_0461/A/807:815,
1/A/849:856		No text annotation
geometric
IL_4V88_425
NA
IL_8PJ4_0471/A/874:876,
1/A/910:912		Isolated non-canonical cWW pair
geometric
IL_4E48_003
IL_01003.4
IL_8PJ4_0481/A/877:879,
1/A/907:909		Isolated non-canonical cWW pair
geometric
IL_3D0U_006
IL_01003.4
IL_8PJ4_0511/A/922:923,
1/A/1019:1022		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_8PJ4_1041/A/925:926,
1/A/1015:1017		Single bulged U
geometric
IL_6UFH_004
IL_97561.4
IL_8PJ4_1091/A/928:931,
1/A/1010:1013		Tandem non-canonical cWW pairs
homologous
IL_8P9A_419
IL_15225.2
IL_8PJ4_0541/A/931:935,
1/A/1007:1010		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_8PJ4_0551/A/942:945,
1/A/981:984		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_8PJ4_0561/A/952:956,
1/A/967:974		Kink-turn
homologous
IL_4V88_434
NA
IL_8PJ4_0571/A/1042:1047,
1/A/1071:1073		No text annotation
homologous
IL_8C3A_441
NA
IL_8PJ4_0581/A/1047:1051,
1/A/1067:1071		tSH-tHW-tHS
geometric
IL_4V88_436
NA
IL_8PJ4_0591/A/1091:1093,
1/A/1152:1158		No text annotation
homologous
IL_8C3A_443
NA
IL_8PJ4_0601/A/1098:1101,
1/A/1131:1134		Tandem non-canonical cWW pairs
geometric
IL_4V88_438
NA
IL_8PJ4_0611/A/1101:1103,
1/A/1129:1131		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_01003.4
IL_8PJ4_0621/A/1108:1110,
1/A/1123:1124		Minor groove platform
geometric
IL_4V88_412
NA
IL_8PJ4_0631/A/1168:1175,
1/A/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_8C3A_446
NA
IL_8PJ4_0641/A/1203:1204,
1/A/1694:1696		Single bulged A
homologous
IL_8C3A_447
NA
IL_8PJ4_0651/A/1206:1208,
1/A/1691:1692		Single bulged G
homologous
IL_8C3A_448
NA
IL_8PJ4_0661/A/1214:1217,
1/A/1681:1685		C-loop
homologous
IL_8C3A_449
NA
IL_8PJ4_0671/A/1230:1232,
1/A/1526:1528		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_8PJ4_0681/A/1235:1236,
1/A/1521:1523		Minor groove platform
homologous
IL_8C3A_451
NA
IL_8PJ4_0691/A/1270:1272,
1/A/1510:1512		Isolated non-canonical cWW pair
geometric
IL_5MWI_006
NA
IL_8PJ4_1101/A/1282:1287,
1/A/1314:1315		No text annotation
geometric
IL_4V9F_009
IL_10396.1
IL_8PJ4_1111/A/1282:1290,
1/A/1309:1315		No text annotation
IL_8PJ4_0711/A/1287:1290,
1/A/1309:1314		No text annotation
IL_8PJ4_0721/A/1291:1293,
1/A/1306:1308		Other IL
homologous
IL_8C3A_454
NA
IL_8PJ4_0731/A/1325:1327,
1/A/1502:1503		Single bulged U
homologous
IL_8C3A_455
NA
IL_8PJ4_0741/A/1329:1333,
1/A/1498:1500		No text annotation
homologous
IL_8C3A_456
NA
IL_8PJ4_1061/A/1329:1335,
1/A/1492:1500		No text annotation
homologous
IL_8P9A_439
IL_99893.1
IL_8PJ4_0751/A/1333:1335,
1/A/1492:1498		Minor groove platform with extra cWW
geometric
IL_4V88_451
NA
IL_8PJ4_0761/A/1337:1338,
1/A/1488:1490		Single bulged A
homologous
IL_8C3A_458
NA
IL_8PJ4_0771/A/1347:1349,
1/A/1380:1382		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_8PJ4_1071/A/1363:1365,
1/A/1374:1375		Minor groove platform
homologous
IL_8C3A_460
NA
IL_8PJ4_0791/A/1395:1399,
1/A/1447:1450		No text annotation
homologous
IL_8C3A_461
NA
IL_8PJ4_0801/A/1402:1405,
1/A/1441:1444		Minor groove platform
homologous
IL_4V88_456
NA
IL_8PJ4_0811/A/1408:1409,
1/A/1432:1438		Multiple bulged bases
geometric
IL_1R3E_002
IL_05670.1
IL_8PJ4_0821/A/1412:1413,
1/A/1427:1429		Single bulged G
geometric
IL_5J7L_019
NA
IL_8PJ4_0831/A/1537:1539,
1/A/1594:1596		Isolated non-canonical cWW pair
geometric
IL_3TD0_001
NA
IL_8PJ4_1081/A/1541:1550,
1/A/1582:1592		No text annotation
IL_8PJ4_0841/A/1550:1558,
1/A/1577:1582		180 degree turn
geometric
IL_5J7L_055
NA
IL_8PJ4_0851/A/1560:1562,
1/A/1573:1575		Isolated non-canonical cWW pair
homologous
IL_8C3A_468
NA
IL_8PJ4_0861/A/1604:1610,
1/A/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_8PJ4_0871/A/1700:1702,
1/A/1833:1836		No text annotation
homologous
IL_8C3A_470
NA
IL_8PJ4_0881/A/1702:1705,
1/A/1829:1833		No text annotation
geometric
IL_4V88_464
NA
IL_8PJ4_0891/A/1706:1708,
1/A/1826:1828		Isolated non-canonical cWW pair
geometric
IL_4E48_004
IL_01003.4
IL_8PJ4_0901/A/1708:1711,
1/A/1822:1826		No text annotation
IL_8PJ4_0911/A/1714:1716,
1/A/1817:1819		Isolated non-canonical cWW pair
homologous
IL_8C3A_474
NA
IL_8PJ4_0921/A/1717:1720,
1/A/1813:1816		Double sheared
homologous
IL_8C3A_475
NA
IL_8PJ4_0941/A/1729:1731,
1/A/1803:1805		Isolated non-canonical cWW pair
homologous
IL_8C3A_477
NA
IL_8PJ4_0951/A/1733:1736,
1/A/1798:1801		Double sheared
homologous
IL_8C3A_478
NA
IL_8PJ4_0961/A/1739:1741,
1/A/1793:1795		Isolated non-canonical cWW pair
geometric
IL_4E48_002
IL_01003.4
IL_8PJ4_0971/A/1742:1746,
1/A/1788:1792		Triple sheared
homologous
IL_8C3A_480
NA
IL_8PJ4_0981/A/1749:1751,
1/A/1784:1785		Single stack bend
geometric
IL_7KGA_003
IL_15011.3

Problematic loops

#loop idProblemSequence
IL_8PJ4_002Isolated non-canonical cWW pair
IL_8PJ4_012No text annotation
IL_8PJ4_014No text annotation
IL_8PJ4_015No text annotation
IL_8PJ4_016No text annotation
IL_8PJ4_019No text annotation
IL_8PJ4_041No text annotation
IL_8PJ4_042No text annotation
IL_8PJ4_043No text annotation
IL_8PJ4_103No text annotation
IL_8PJ4_049Isolated cWH basepair
IL_8PJ4_050No text annotation
IL_8PJ4_052Isolated cWH basepair
IL_8PJ4_053No text annotation
IL_8PJ4_070No text annotation
IL_8PJ4_105No text annotation
IL_8PJ4_078Minor groove platform with extra cWW
IL_8PJ4_093Single bulged U

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8PJ4_0111/A/40:41,
1/A/481:487,
1/A/512:514		No text annotation
geometric
J3_8C3A_082
NA
J3_8PJ4_0121/A/40:47,
1/A/479:487,
1/A/512:514		No text annotation
homologous
J3_8P9A_069
J3_63856.1
J3_8PJ4_0131/A/682:685,
1/A/917:922,
1/A/1022:1023		No text annotation
J3_8PJ4_0141/A/682:685,
1/A/917:923,
1/A/1019:1023		No text annotation
J3_8PJ4_0011/A/816:819,
1/A/829:831,
1/A/843:848		No text annotation
homologous
J3_4V88_032
NA
J3_8PJ4_0021/A/938:941,
1/A/985:993,
1/A/1000:1004		No text annotation
homologous
J3_4V88_033
NA
J3_8PJ4_0031/A/1094:1096,
1/A/1136:1140,
1/A/1147:1151		No text annotation
J3_8PJ4_0041/A/1218:1221,
1/A/1645:1651,
1/A/1673:1680		No text annotation
homologous
J3_4V88_035
NA
J3_8PJ4_0051/A/1225:1228,
1/A/1530:1532,
1/A/1638:1641		No text annotation
homologous
J3_8C3A_039
NA
J3_8PJ4_0061/A/1237:1244,
1/A/1255:1266,
1/A/1516:1520		No text annotation
homologous
J3_8C3A_040
NA
J3_8PJ4_0071/A/1272:1277,
1/A/1320:1324,
1/A/1504:1510		No text annotation
homologous
J3_8C3A_041
NA
J3_8PJ4_0081/A/1340:1345,
1/A/1384:1389,
1/A/1481:1486		No text annotation
homologous
J3_4V88_039
NA
J3_8PJ4_0151/A/1350:1351,
1/A/1360:1363,
1/A/1375:1379		No text annotation
homologous
J3_8C3A_085
NA
J3_8PJ4_0091/A/1391:1395,
1/A/1450:1456,
1/A/1470:1479		No text annotation
J3_8PJ4_0101/A/1532:1536,
1/A/1597:1604,
1/A/1635:1638		No text annotation
geometric
J3_8C3A_044
NA
J4_8PJ4_0011/A/98:106,
1/A/355:357,
1/A/405:409,
1/A/431:432		No text annotation
homologous
J4_8P9A_021
J4_15241.2
J4_8PJ4_0021/A/671:673,
1/A/1032:1037,
1/A/1078:1089,
1/A/1160:1161		No text annotation
homologous
J4_8C3A_022
NA
J4_8PJ4_0031/w/7:10,
1/w/25:27,
1/w/43:49,
1/w/65:66		tRNA junction
homologous
J4_7YSE_001
J4_95067.1
J5_8PJ4_0011/A/30:34,
1/A/521:527,
1/A/558:563,
1/A/592:595,
1/A/641:644		No text annotation
homologous
J5_8C3A_018
NA
J5_8PJ4_0021/A/30:34,
1/A/521:527,
1/A/558:565,
1/A/585:595,
1/A/641:644		No text annotation
J5_8PJ4_0031/A/53:56,
1/A/89:96,
1/A/434:436,
1/A/457:459,
1/A/470:474		No text annotation
homologous
J5_8C3A_020
NA
J5_8PJ4_0041/A/123:129,
1/A/183:185,
1/A/214:215,
1/A/310:312,
1/A/337:341		No text annotation

Problematic loops

#loop idProblemSequence
J3_8PJ4_016No text annotation

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