RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6ZQD_0041/D3/70:81No text annotation
homologous
HL_4V88_187
NA
HL_6ZQD_0051/D3/154:160GNRA related
homologous
HL_4V88_188
NA
HL_6ZQD_0081/D3/243:250T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_6ZQD_0101/D3/330:338GNRA related
homologous
HL_4V88_193
NA
HL_6ZQD_0111/D3/368:373GNRA
geometric
HL_6WPI_001
HL_34789.4
HL_6ZQD_0121/D3/393:404No text annotation
homologous
HL_4V88_195
NA
HL_6ZQD_0131/D3/414:419UNCG
homologous
HL_4V88_196
NA
HL_6ZQD_0141/D3/450:456No text annotation
homologous
HL_4V88_197
NA
HL_6ZQD_0151/D3/491:496No text annotation
geometric
HL_2Y9H_003
HL_75660.7
HL_6ZQD_0161/D3/520:532No text annotation
geometric
HL_4V88_199
NA
HL_6ZQD_0171/D3/561:566No text annotation
geometric
HL_5TBW_006
NA
HL_6ZQD_0191/D3/764:772No text annotation
homologous
HL_4V88_203
NA
HL_6ZQD_0221/D3/900:909No text annotation
homologous
HL_4V88_206
NA
HL_6ZQD_0231/D3/937:942GNRA
homologous
HL_4V88_207
NA
HL_6ZQD_0241/D3/997:1007No text annotation
geometric
HL_4WF9_011
HL_75660.7
HL_6ZQD_0251/D3/1055:1064No text annotation
geometric
HL_4V88_198
NA
HL_6ZQD_0261/D3/1084:1089GNRA
homologous
HL_4V88_210
NA
HL_6ZQD_0301/D3/1594:1602No text annotation
HL_6ZQD_0311/D3/1629:1636No text annotation
HL_6ZQD_0331/D3/1778:1783Mini UNCG
geometric
HL_6AAX_001
HL_12626.2

Problematic loops

#loop idProblemSequence
HL_6ZQD_001No text annotation
HL_6ZQD_002No text annotation
HL_6ZQD_003No text annotation
HL_6ZQD_038No text annotation
HL_6ZQD_006No text annotation
HL_6ZQD_007UNCG
HL_6ZQD_009Mini UNCG
HL_6ZQD_018No text annotation
HL_6ZQD_020No text annotation
HL_6ZQD_021Externally structured
HL_6ZQD_027No text annotation
HL_6ZQD_028GNRA
HL_6ZQD_029No text annotation
HL_6ZQD_032GNRA
HL_6ZQD_034No text annotation
HL_6ZQD_035No text annotation
HL_6ZQD_036No text annotation
HL_6ZQD_037No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6ZQD_0041/D3/24:26,
1/D3/600:601		Single bulged C
homologous
IL_4V88_384
NA
IL_6ZQD_0051/D3/35:37,
1/D3/471:473		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_6ZQD_0061/D3/37:41,
1/D3/466:471		No text annotation
IL_6ZQD_0071/D3/50:52,
1/D3/428:429		Minor groove platform
homologous
IL_4V88_388
NA
IL_6ZQD_0081/D3/58:63,
1/D3/87:89		No text annotation
homologous
IL_4V88_389
NA
IL_6ZQD_0091/D3/64:69,
1/D3/82:86		No text annotation
homologous
IL_4V88_390
NA
IL_6ZQD_0101/D3/109:112,
1/D3/302:305		Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA
IL_6ZQD_0111/D3/113:116,
1/D3/300:301		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_6ZQD_0121/D3/117:122,
1/D3/295:299		No text annotation
homologous
IL_4V88_393
NA
IL_6ZQD_0821/D3/144:149,
1/D3/165:171		tWH-tWH-tHW-tHW
geometric
IL_4LFB_009
IL_00680.1
IL_6ZQD_0141/D3/150:152,
1/D3/162:164		Isolated cWH basepair
geometric
IL_6RA4_002
IL_10892.2
IL_6ZQD_0151/D3/186:189,
1/D3/196:199		Double sheared
homologous
IL_4V88_396
NA
IL_6ZQD_0161/D3/204:206,
1/D3/259:263		No text annotation
homologous
IL_8P9A_386
IL_36931.2
IL_6ZQD_0171/D3/206:209,
1/D3/256:259		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001
IL_15225.2
IL_6ZQD_0181/D3/265:267,
1/D3/288:289		Single bulged A
homologous
IL_4V88_399
NA
IL_6ZQD_0191/D3/270:273,
1/D3/283:285		No text annotation
homologous
IL_4V88_400
NA
IL_6ZQD_0201/D3/275:276,
1/D3/279:281		Single bulged U
homologous
IL_4V88_401
NA
IL_6ZQD_0211/D3/311:316,
1/D3/348:355		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_6ZQD_0221/D3/318:323,
1/D3/345:346		No text annotation
geometric
IL_5Y58_001
IL_37738.1
IL_6ZQD_0231/D3/363:365,
1/D3/376:381		No text annotation
homologous
IL_4V88_404
NA
IL_6ZQD_0241/D3/389:391,
1/D3/406:408		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_6ZQD_0251/D3/411:413,
1/D3/420:422		Isolated near basepair
homologous
IL_4V88_406
NA
IL_6ZQD_0261/D3/439:441,
1/D3/463:464		Single bulged U
homologous
IL_4V88_407
NA
IL_6ZQD_0271/D3/443:447,
1/D3/460:461		C-loop
geometric
IL_5J7L_018
NA
IL_6ZQD_0281/D3/447:448,
1/D3/458:460		Single bulged G
geometric
IL_5J7L_019
NA
IL_6ZQD_0291/D3/482:483,
1/D3/504:506		Single bulged A
homologous
IL_4V88_409
NA
IL_6ZQD_0301/D3/517:518,
1/D3/533:535		Minor groove platform
geometric
IL_4UYK_001
IL_34520.3
IL_6ZQD_0311/D3/518:520,
1/D3/532:533		Minor groove platform
homologous
IL_4V88_412
NA
IL_6ZQD_0321/D3/551:552,
1/D3/584:587		Multiple bulged bases
geometric
IL_3IGI_013
IL_44609.2
IL_6ZQD_0331/D3/552:559,
1/D3/568:584		No text annotation
IL_6ZQD_0341/D3/616:622,
1/D3/1104:1105		No text annotation
homologous
IL_4V88_416
NA
IL_6ZQD_0351/D3/624:626,
1/D3/973:975		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_6ZQD_0361/D3/627:631,
1/D3/968:972		No text annotation
IL_6ZQD_0371/D3/646:648,
1/D3/686:688		Isolated non-canonical cWW pair
homologous
IL_4V88_419
NA
IL_6ZQD_0841/D3/652:657,
1/D3/677:682		No text annotation
IL_6ZQD_0391/D3/703:705,
1/D3/733:735		Isolated cWH basepair
geometric
IL_3R1C_012
IL_10892.2
IL_6ZQD_0911/D3/746:747,
1/D3/802:805		Minor groove platform
geometric
IL_9DFE_073
IL_24264.1
IL_6ZQD_0431/D3/748:750,
1/D3/799:801		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_6ZQD_0441/D3/751:759,
1/D3/791:798		No text annotation
homologous
IL_8C3A_503
NA
IL_6ZQD_0451/D3/865:866,
1/D3/962:965		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_6ZQD_0851/D3/867:869,
1/D3/958:961		Isolated non-canonical cWW pair
homologous
IL_8P9A_418
IL_01003.3
IL_6ZQD_0461/D3/868:869,
1/D3/958:960		Single bulged U
geometric
IL_7KVT_002
IL_97561.3
IL_6ZQD_0861/D3/871:873,
1/D3/954:956		Isolated non-canonical cWW pair
geometric
IL_2R8S_001
IL_01003.3
IL_6ZQD_0481/D3/874:878,
1/D3/950:953		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_6ZQD_0491/D3/885:888,
1/D3/924:927		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_6ZQD_0501/D3/893:895,
1/D3/917:919		Isolated non-canonical cWW pair
geometric
IL_2OE5_001
IL_71625.3
IL_6ZQD_0871/D3/893:899,
1/D3/910:919		No text annotation
homologous
IL_8P9A_422
IL_57741.1
IL_6ZQD_0511/D3/895:899,
1/D3/910:917		Kink-turn
homologous
IL_4V88_434
NA
IL_6ZQD_0521/D3/985:990,
1/D3/1014:1016		Other IL
geometric
IL_4V88_435
NA
IL_6ZQD_0531/D3/990:994,
1/D3/1010:1014		tSH-tHW-tHS
geometric
IL_7A0S_049
IL_05821.1
IL_6ZQD_0541/D3/1034:1036,
1/D3/1095:1101		No text annotation
homologous
IL_4V88_437
NA
IL_6ZQD_0551/D3/1041:1044,
1/D3/1074:1077		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_6ZQD_0561/D3/1051:1053,
1/D3/1066:1067		Single stack bend
geometric
IL_4WF9_007
IL_15011.2
IL_6ZQD_0571/D3/1117:1119,
1/D4/6:7		No text annotation
IL_6ZQD_0881/D3/1150:1151,
1/D3/1627:1640		No text annotation
IL_6ZQD_0591/D3/1157:1160,
1/D3/1617:1621		C-loop
homologous
IL_4V88_443
NA
IL_6ZQD_0601/D3/1173:1175,
1/D3/1464:1466		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_6ZQD_0611/D3/1495:1498,
1/D3/1509:1512		Tandem non-canonical cWW pairs
homologous
IL_4V88_461
NA
IL_6ZQD_0621/D3/1540:1545,
1/D3/1566:1571		No text annotation
homologous
IL_4V88_462
NA
IL_6ZQD_0631/D3/1550:1552,
1/D3/1559:1561		Isolated non-canonical cWW pair
geometric
IL_3SZX_003
IL_01003.3
IL_6ZQD_0641/D3/1650:1652,
1/D3/1748:1750		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_6ZQD_0741/D4/78:85,
1/D4/325:329		No text annotation
IL_6ZQD_0901/D4/85:96,
1/D4/320:325		No text annotation
IL_6ZQD_0751/D4/97:98,
1/D4/317:319		No text annotation
IL_6ZQD_0761/D4/111:115,
1/D4/252:259		No text annotation
IL_6ZQD_0771/D4/139:142,
1/D4/169:171		No text annotation
IL_6ZQD_0781/D4/144:146,
1/D4/166:167		No text annotation
IL_6ZQD_0791/D4/148:150,
1/D4/163:164		No text annotation

Problematic loops

#loop idProblemSequence
IL_6ZQD_001Single bulged G
IL_6ZQD_002No text annotation
IL_6ZQD_081No text annotation
IL_6ZQD_003Single stack bend
IL_6ZQD_013tWH-tWH-tHW-tHW
IL_6ZQD_083Isolated non-canonical cWW pair
IL_6ZQD_038No text annotation
IL_6ZQD_040Tandem non-canonical cWW pairs
IL_6ZQD_041Tandem non-canonical cWW pairs
IL_6ZQD_042Minor groove platform with extra cWW
IL_6ZQD_047Tandem non-canonical cWW pairs
IL_6ZQD_058Single bulged U
IL_6ZQD_065No text annotation
IL_6ZQD_066Isolated non-canonical cWW pair
IL_6ZQD_067Double sheared
IL_6ZQD_068Isolated non-canonical cWW pair
IL_6ZQD_069Tandem non-canonical cWW pairs
IL_6ZQD_070No text annotation
IL_6ZQD_071No text annotation
IL_6ZQD_089No text annotation
IL_6ZQD_072No text annotation
IL_6ZQD_073Single stack bend
IL_6ZQD_080No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6ZQD_0011/D3/41:48,
1/D3/431:439,
1/D3/464:466		No text annotation
J3_6ZQD_0021/D3/633:635,
1/D3/861:865,
1/D3/965:966		No text annotation
geometric
J3_4V88_080
NA
J3_6ZQD_0101/D3/633:635,
1/D3/861:866,
1/D3/962:966		No text annotation
homologous
J3_8P9A_072
J3_17385.5
J3_6ZQD_0041/D3/881:884,
1/D3/928:936,
1/D3/943:947		No text annotation
homologous
J3_4V88_033
NA
J3_6ZQD_0051/D3/1037:1039,
1/D3/1079:1083,
1/D3/1090:1094		No text annotation
homologous
J3_4V88_034
NA
J3_6ZQD_0061/D3/1150:1151,
1/D3/1627:1629,
1/D3/1636:1640		No text annotation
J3_6ZQD_0121/D3/1161:1163,
1/D3/1582:1587,
1/D3/1609:1616		No text annotation
J3_6ZQD_0071/D3/1168:1171,
1/D3/1468:1470,
1/D3/1574:1577		No text annotation
homologous
J3_8C3A_039
NA
J3_6ZQD_0081/D3/1470:1474,
1/D3/1533:1540,
1/D3/1571:1574		No text annotation
homologous
J3_4V88_041
NA
J4_6ZQD_0011/D3/99:107,
1/D3/307:309,
1/D3/357:361,
1/D3/383:384		No text annotation
homologous
J4_8P9A_021
J4_15241.2
J4_6ZQD_0031/D3/622:624,
1/D3/975:980,
1/D3/1021:1032,
1/D3/1103:1104		No text annotation
homologous
J4_8P9A_022
J4_14595.1
J5_6ZQD_0011/D3/31:35,
1/D3/473:479,
1/D3/509:516,
1/D3/536:546,
1/D3/592:595		No text annotation
J5_6ZQD_0021/D3/54:57,
1/D3/90:97,
1/D3/386:388,
1/D3/409:411,
1/D3/422:426		No text annotation
homologous
J5_8C3A_020
NA

Problematic loops

#loop idProblemSequence
J3_6ZQD_003No text annotation
J3_6ZQD_011No text annotation
J3_6ZQD_009No text annotation
J4_6ZQD_002No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1049 s