RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6DZK_0011/A/16:26No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_6DZK_0031/A/155:160GNRA
homologous
HL_5J7L_003
NA
HL_6DZK_0041/A/191:196No text annotation
geometric
HL_5J7L_143
NA
HL_6DZK_0051/A/213:218No text annotation
geometric
HL_2Y9H_003
HL_75660.7
HL_6DZK_0061/A/259:267GNRA related
homologous
HL_5J7L_006
NA
HL_6DZK_0071/A/296:301GNRA
homologous
HL_6CZR_078
NA
HL_6DZK_0081/A/320:333No text annotation
HL_6DZK_0091/A/342:347UNCG
homologous
HL_5J7L_009
NA
HL_6DZK_0101/A/379:384GNRA
homologous
HL_4LFB_010
HL_34789.4
HL_6DZK_0111/A/419:424UNCG
homologous
HL_5J7L_011
NA
HL_6DZK_0121/A/454:459No text annotation
geometric
HL_5TBW_006
NA
HL_6DZK_0131/A/502:507No text annotation
geometric
HL_5J7L_143
NA
HL_6DZK_0141/A/597:603GNRA-like with tWH
homologous
HL_4LFB_014
HL_86621.1
HL_6DZK_0151/A/669:678No text annotation
homologous
HL_6CZR_086
NA
HL_6DZK_0161/A/706:711GNRA
homologous
HL_4LFB_016
HL_34789.4
HL_6DZK_0171/A/766:776No text annotation
homologous
HL_4LFB_017
HL_38491.2
HL_6DZK_0191/A/844:849GNRA
homologous
HL_5J7L_019
NA
HL_6DZK_0201/A/879:884GNRA
homologous
HL_6CZR_091
NA
HL_6DZK_0211/A/945:954No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_6DZK_0221/A/995:1000GNRA
homologous
HL_4LFB_022
HL_34789.4
HL_6DZK_0241/A/1056:1061GNRA
homologous
HL_5J7L_023
NA
HL_6DZK_0251/A/1069:1076T-loop related
homologous
HL_6CZR_096
NA
HL_6DZK_0271/A/1146:1152GNRA
homologous
HL_4LFB_027
HL_34789.4
HL_6DZK_0281/A/1246:1251GNRA
homologous
HL_4LFB_028
HL_34789.4
HL_6DZK_0291/A/1296:1305T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_93658.1
HL_6DZK_0301/A/1338:1349No text annotation
homologous
HL_4LFB_030
HL_86432.1
HL_6DZK_0321/A/1499:1504GNRA
homologous
HL_6CZR_103
NA

Problematic loops

#loop idProblemSequence
HL_6DZK_002No text annotation
HL_6DZK_018No text annotation
HL_6DZK_023No text annotation
HL_6DZK_026No text annotation
HL_6DZK_031Externally structured

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6DZK_0011/A/34:36,
1/A/532:533		Single bulged G
homologous
IL_4LFB_001
IL_28408.2
IL_6DZK_0021/A/48:49,
1/A/396:398		Single bulged A
homologous
IL_4LFB_002
IL_14190.2
IL_6DZK_0031/A/51:56,
1/A/359:361		No text annotation
homologous
IL_5J7L_003
NA
IL_6DZK_0041/A/58:60,
1/A/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_34520.3
IL_6DZK_0051/A/67:70,
1/A/99:100		Multiple bulged bases
homologous
IL_4LFB_005
IL_71421.2
IL_6DZK_0061/A/71:73,
1/A/95:98		Minor groove platform with extra cWW
homologous
IL_5J7L_006
NA
IL_6DZK_0071/A/74:77,
1/A/93:94		Minor groove platform
homologous
IL_5J7L_007
NA
IL_6DZK_0091/A/125:128,
1/A/231:232		Multiple bulged bases
homologous
IL_4LFB_007
IL_75289.1
IL_6DZK_0101/A/129:133,
1/A/227:230		No text annotation
homologous
IL_4LFB_008
IL_60988.2
IL_6DZK_0111/A/144:150,
1/A/165:172		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
NA
IL_6DZK_0121/A/187:188,
1/A/199:201		Single bulged U
geometric
IL_4V88_469
NA
IL_6DZK_0131/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_6DZK_0141/A/249:252,
1/A/274:275		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_6DZK_0151/A/292:293,
1/A/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_6DZK_0161/A/367:369,
1/A/392:393		Single bulged U
geometric
IL_4LFB_014
IL_97561.3
IL_6DZK_0171/A/371:375,
1/A/389:390		C-loop
homologous
IL_5J7L_018
NA
IL_6DZK_0181/A/375:376,
1/A/387:389		Single bulged G
geometric
IL_5J7L_019
NA
IL_6DZK_0191/A/409:416,
1/A/427:433		No text annotation
homologous
IL_4LFB_017
IL_62329.1
IL_6DZK_0201/A/440:442,
1/A/472:477		No text annotation
homologous
IL_5J7L_021
NA
IL_6DZK_0211/A/446:450,
1/A/463:468		6x5 Sarcin-Ricin; G-bulge
geometric
IL_4LFB_018
IL_82100.1
IL_6DZK_0221/A/450:453,
1/A/460:463		No text annotation
IL_6DZK_0231/A/484:491,
1/A/520:521		SSU/LSU pseudoknot
homologous
IL_6CZR_132
NA
IL_6DZK_0241/A/495:501,
1/A/508:516		Kink-turn related
geometric
IL_4V88_415
NA
IL_6DZK_0251/A/560:564,
1/A/737:741		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_6DZK_0261/A/574:576,
1/A/624:625		Major groove platform
homologous
IL_4LFB_024
IL_48076.8
IL_6DZK_0271/A/577:578,
1/A/620:623		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_73108.2
IL_6DZK_0281/A/585:591,
1/A/609:613		No text annotation
geometric
IL_8C3A_433
NA
IL_6DZK_0291/A/634:635,
1/A/731:734		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_6DZK_0301/A/637:638,
1/A/727:729		Major groove platform
homologous
IL_6CZR_140
NA
IL_6DZK_0311/A/642:646,
1/A/720:723		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
NA
IL_6DZK_0321/A/653:658,
1/A/692:697		No text annotation
geometric
IL_5J7L_034
NA
IL_6DZK_0721/A/653:660,
1/A/690:697		No text annotation
IL_6DZK_0331/A/664:668,
1/A/679:686		Kink-turn
homologous
IL_5J7L_035
NA
IL_6DZK_0341/A/754:758,
1/A/784:785		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_6DZK_0351/A/759:763,
1/A/779:783		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_05821.1
IL_6DZK_0361/A/869:876,
1/A/887:892		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_84044.1
IL_6DZK_0371/A/904:905,
1/A/1376:1378		Single bulged A
homologous
IL_4LFB_035
IL_14190.2
IL_6DZK_0381/A/907:909,
1/A/1373:1374		Single bulged G
homologous
IL_5J7L_040
NA
IL_6DZK_0391/A/935:936,
1/A/1207:1209		Minor groove platform
homologous
IL_4LFB_038
IL_34520.3
IL_6DZK_0401/A/975:979,
1/A/1024:1025		Minor groove platform
geometric
IL_5J7L_043
NA
IL_6DZK_0411/A/1028:1030,
1/A/1189:1190		No text annotation
homologous
IL_6CZR_152
NA
IL_6DZK_0421/A/1032:1036,
1/A/1185:1187		Isolated cWS basepair
homologous
IL_4LFB_044
IL_82453.1
IL_6DZK_0731/A/1037:1038,
1/A/1180:1184		Minor groove platform
homologous
IL_5J7L_048
NA
IL_6DZK_0441/A/1040:1041,
1/A/1176:1178		Single bulged A
homologous
IL_5J7L_049
NA
IL_6DZK_0451/A/1041:1043,
1/A/1174:1176		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_68118.3
IL_6DZK_0461/A/1104:1108,
1/A/1125:1130		No text annotation
homologous
IL_5J7L_051
NA
IL_6DZK_0741/A/1109:1112,
1/A/1123:1124		Minor groove platform
homologous
IL_5J7L_052
NA
IL_6DZK_0481/A/1139:1142,
1/A/1156:1162		No text annotation
geometric
IL_5J7L_053
NA
IL_6DZK_0701/A/1228:1234,
1/A/1265:1272		No text annotation
homologous
IL_5J7L_054
NA
IL_6DZK_0501/A/1236:1239,
1/A/1258:1263		180 degree turn
homologous
IL_4LFB_052
IL_08849.1
IL_6DZK_0511/A/1240:1245,
1/A/1252:1257		No text annotation
IL_6DZK_0521/A/1285:1290,
1/A/1311:1316		No text annotation
geometric
IL_4LFB_055
IL_57885.2
IL_6DZK_0531/A/1382:1384,
1/A/1485:1488		No text annotation
geometric
IL_4V88_463
NA
IL_6DZK_0541/A/1384:1387,
1/A/1481:1485		No text annotation
geometric
IL_4V88_464
NA
IL_6DZK_0551/A/1388:1390,
1/A/1478:1480		Isolated non-canonical cWW pair
geometric
IL_5MWI_004
IL_01003.3
IL_6DZK_0561/A/1390:1392,
1/A/1475:1478		Isolated non-canonical cWW pair
geometric
IL_5J7L_009
NA
IL_6DZK_0571/A/1395:1397,
1/A/1470:1472		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6DZK_0581/A/1399:1402,
1/A/1465:1468		Double sheared
homologous
IL_5J7L_062
NA
IL_6DZK_0591/A/1407:1410,
1/A/1458:1460		No text annotation
geometric
IL_4P3T_002
NA
IL_6DZK_0711/A/1407:1411,
1/A/1456:1460		Partly complementary
geometric
IL_8D29_010
IL_71154.3
IL_6DZK_0601/A/1410:1411,
1/A/1456:1458		Single stack bend
geometric
IL_7A0S_054
IL_15011.2
IL_6DZK_0611/A/1413:1418,
1/A/1450:1454		Triple sheared related
geometric
IL_5J7L_063
NA
IL_6DZK_0621/A/1418:1420,
1/A/1448:1450		Isolated non-canonical cWW pair
homologous
IL_4LFB_063
IL_01003.3
IL_6DZK_0631/A/1423:1426,
1/A/1443:1445		Isolated tHS basepair with bulges
geometric
IL_7RQB_082
NA
IL_6DZK_0641/A/1428:1431,
1/A/1439:1441		No text annotation
homologous
IL_5J7L_065
NA
IL_6DZK_0651/A/1432:1433,
1/A/1436:1438		No text annotation
geometric
IL_8GLP_209
IL_97561.3

Problematic loops

#loop idProblemSequence
IL_6DZK_066Isolated non-canonical cWW pair
IL_6DZK_067No text annotation
IL_6DZK_008Major groove platform with extra pair
IL_6DZK_068Isolated non-canonical cWW pair
IL_6DZK_069No text annotation
IL_6DZK_043No text annotation
IL_6DZK_047No text annotation
IL_6DZK_049No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6DZK_0011/A/50:51,
1/A/361:367,
1/A/393:395		No text annotation
homologous
J3_5J7L_001
NA
J3_6DZK_0131/A/50:56,
1/A/359:367,
1/A/393:395		No text annotation
homologous
J3_4LFB_014
J3_63856.1
J3_6DZK_0021/A/566:568,
1/A/631:634,
1/A/734:735		No text annotation
geometric
J3_5J7L_002
NA
J3_6DZK_0141/A/566:568,
1/A/631:635,
1/A/731:735		No text annotation
homologous
J3_4LFB_015
J3_17385.5
J3_6DZK_0031/A/652:653,
1/A/697:705,
1/A/712:714		No text annotation
homologous
J3_6CZR_017
NA
J3_6DZK_0041/A/806:809,
1/A/839:843,
1/A/850:856		No text annotation
J3_6DZK_0151/A/915:921,
1/A/1326:1332,
1/A/1355:1367		No text annotation
J3_6DZK_0161/A/925:928,
1/A/1216:1218,
1/A/1319:1322		No text annotation
homologous
J3_4LFB_003
J3_44359.1
J3_6DZK_0061/A/937:944,
1/A/955:966,
1/A/1202:1206		No text annotation
homologous
J3_4LFB_004
J3_88451.1
J3_6DZK_0071/A/972:975,
1/A/1025:1027,
1/A/1191:1196		No text annotation
homologous
J3_4LFB_005
J3_84394.1
J3_6DZK_0171/A/972:979,
1/A/1024:1027,
1/A/1191:1196		No text annotation
homologous
J3_4LFB_016
J3_28881.1
J3_6DZK_0091/A/1043:1048,
1/A/1087:1093,
1/A/1168:1174		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J3_6DZK_0201/A/1053:1054,
1/A/1063:1067,
1/A/1078:1082		No text annotation
homologous
J3_5J7L_009
NA
J3_6DZK_0211/A/1096:1098,
1/A/1136:1139,
1/A/1162:1165		No text annotation
geometric
J3_5J7L_010
NA
J3_6DZK_0221/A/1096:1098,
1/A/1136:1142,
1/A/1156:1165		No text annotation
homologous
J3_5J7L_054
NA
J3_6DZK_0121/A/1218:1222,
1/A/1278:1285,
1/A/1316:1319		No text annotation
homologous
J3_4LFB_009
J3_03192.1
J4_6DZK_0011/A/111:119,
1/A/238:240,
1/A/286:289,
1/A/311:312		No text annotation
J4_6DZK_0021/A/140:141,
1/A/175:181,
1/A/207:212,
1/A/219:220		No text annotation
J4_6DZK_0031/A/549:557,
1/A/744:749,
1/A/790:801,
1/A/861:863		No text annotation
J5_6DZK_0011/A/40:43,
1/A/403:406,
1/A/436:440,
1/A/477:480,
1/A/525:528		No text annotation
homologous
J5_5J7L_001
NA
J5_6DZK_0021/A/40:43,
1/A/403:406,
1/A/436:442,
1/A/472:480,
1/A/525:528		No text annotation
homologous
J5_5J7L_002
NA
J5_6DZK_0031/A/62:65,
1/A/102:109,
1/A/314:316,
1/A/337:339,
1/A/350:354		No text annotation
homologous
J5_4LFB_002
J5_58574.1

Problematic loops

#loop idProblemSequence
J3_6DZK_005No text annotation
J3_6DZK_008No text annotation
J3_6DZK_018No text annotation
J3_6DZK_010No text annotation
J3_6DZK_011No text annotation
J3_6DZK_019No text annotation

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