RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4NXN_0011/A/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_4NXN_0371/A/80:89No text annotation
geometric
HL_8KEB_002
HL_65794.5
HL_4NXN_0031/A/158:163GNRA
homologous
HL_4LFB_003
HL_37824.7
HL_4NXN_0041/A/190B:190GNo text annotation
homologous
HL_4LFB_004
HL_48417.5
HL_4NXN_0351/A/201:216Mini UNCG
homologous
HL_4LFB_005
HL_48778.2
HL_4NXN_0061/A/259:267GNRA related
homologous
HL_4LFB_006
HL_84299.4
HL_4NXN_0071/A/296:301GNRA
homologous
HL_4LFB_007
HL_37824.7
HL_4NXN_0081/A/320:333No text annotation
homologous
HL_4LFB_008
HL_81205.3
HL_4NXN_0091/A/342:347UNCG
homologous
HL_4LFB_009
HL_34617.5
HL_4NXN_0101/A/379:384GNRA
homologous
HL_4LFB_010
HL_37824.7
HL_4NXN_0111/A/419:424UNCG
homologous
HL_4LFB_011
HL_34617.5
HL_4NXN_0121/A/458:474GNRA
homologous
HL_4LFB_012
HL_37824.7
HL_4NXN_0131/A/522:527Mini UNCG
geometric
HL_4YAZ_004
HL_48778.2
HL_4NXN_0141/A/617:623No text annotation
homologous
HL_4LFB_014
HL_10453.3
HL_4NXN_0151/A/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_4NXN_0161/A/726:731GNRA
homologous
HL_4LFB_016
HL_37824.7
HL_4NXN_0171/A/786:796No text annotation
homologous
HL_4LFB_017
HL_75293.5
HL_4NXN_0181/A/838:848Mini UNCG
homologous
HL_6CZR_089
NA
HL_4NXN_0191/A/862:867GNRA
homologous
HL_4LFB_019
HL_37824.7
HL_4NXN_0201/A/897:902GNRA
homologous
HL_4LFB_020
HL_37824.7
HL_4NXN_0211/A/963:972No text annotation
homologous
HL_4LFB_021
HL_50779.4
HL_4NXN_0221/A/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.7
HL_4NXN_0231/A/1030:1031No text annotation
homologous
HL_4LFB_023
NA
HL_4NXN_0241/A/1076:1081GNRA
homologous
HL_5J7L_023
HL_37824.7
HL_4NXN_0251/A/1089:1096T-loop related
homologous
HL_4LFB_025
HL_77436.5
HL_4NXN_0261/A/1134:1140No text annotation
homologous
HL_4LFB_026
HL_87954.2
HL_4NXN_0271/A/1165:1171GNRA
homologous
HL_4LFB_027
HL_37824.7
HL_4NXN_0281/A/1265:1270GNRA
homologous
HL_4LFB_028
HL_37824.7
HL_4NXN_0291/A/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_02887.3
HL_4NXN_0301/A/1356:1366No text annotation
homologous
HL_4LFB_030
HL_06226.4
HL_4NXN_0311/A/1449:1454UNCG
homologous
HL_4LFB_031
HL_34617.5
HL_4NXN_0321/A/1515:1520GNRA
homologous
HL_6CZR_103
NA

Problematic loops

#loop idProblemSequence
HL_4NXN_033No text annotation
HL_4NXN_002tRNA anticodon loop
HL_4NXN_034GNRA with near cWW
HL_4NXN_005No text annotation
HL_4NXN_036GNRA with near cWW

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4NXN_0011/A/30:32,
1/A/552:553		Single bulged G
homologous
IL_4LFB_001
IL_00225.13
IL_4NXN_0021/A/44:45,
1/A/396:398		Single bulged A
homologous
IL_4LFB_002
IL_31462.5
IL_4NXN_0031/A/47:52,
1/A/359:361		No text annotation
homologous
IL_4LFB_003
IL_14177.2
IL_4NXN_0041/A/54:56,
1/A/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_51454.2
IL_4NXN_0051/A/63:66,
1/A/103:104		Multiple bulged bases
homologous
IL_4LFB_005
IL_82107.4
IL_4NXN_0061/A/67:69,
1/A/99:102		Isolated non-canonical cWW pair
homologous
IL_4LFB_006
IL_87907.2
IL_4NXN_0091/A/129:131,
1/A/231:232		Multiple bulged bases
homologous
IL_4LFB_007
IL_33761.2
IL_4NXN_0101/A/132:136,
1/A/227:230		No text annotation
homologous
IL_4LFB_008
IL_64231.5
IL_4NXN_0111/A/148:153,
1/A/168:174		tWH-tWH-tHW-tHW
homologous
IL_4LFB_009
IL_12745.1
IL_4NXN_0121/A/186:188,
1/A/190K:191		Isolated non-canonical cWW pair
homologous
IL_4LFB_010
IL_87907.2
IL_4NXN_0131/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
homologous
IL_4LFB_011
IL_46174.3
IL_4NXN_0141/A/249:252,
1/A/274:275		No text annotation
homologous
IL_4LFB_012
IL_47074.2
IL_4NXN_0151/A/292:293,
1/A/304:308		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_4NXN_0161/A/367:369,
1/A/392:393		Single bulged U
homologous
IL_4LFB_014
IL_89505.4
IL_4NXN_0171/A/371:375,
1/A/389:390		C-loop
geometric
IL_4LFB_015
IL_03109.3
IL_4NXN_0181/A/375:376,
1/A/387:389		Single bulged G
homologous
IL_4LFB_016
IL_00225.13
IL_4NXN_0631/A/409:416,
1/A/427:433		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_4NXN_0201/A/446:450,
1/A/483:488		6x5 Sarcin-Ricin; G-bulge
geometric
IL_4LFB_018
IL_88269.4
IL_4NXN_0211/A/450:455,
1/A/477:483		No text annotation
homologous
IL_4LFB_019
IL_31561.1
IL_4NXN_0221/A/504:511,
1/A/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_41203.4
IL_4NXN_0231/A/515:521,
1/A/528:536		Kink-turn related
homologous
IL_4LFB_021
IL_54177.4
IL_4NXN_0241/A/569:575,
1/A/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_4NXN_0251/A/580:584,
1/A/757:761		tSH-tHW-tHS
homologous
IL_4LFB_023
IL_17136.7
IL_4NXN_0261/A/594:596,
1/A/644:645		Major groove platform
homologous
IL_4LFB_024
IL_48076.6
IL_4NXN_0271/A/597:598,
1/A/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_68140.4
IL_4NXN_0281/A/605:612,
1/A/628:633		No text annotation
homologous
IL_4LFB_026
IL_78349.3
IL_4NXN_0291/A/654:655,
1/A/751:754		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_50694.7
IL_4NXN_0301/A/657:658,
1/A/747:749		Major groove platform
homologous
IL_4LFB_028
IL_48076.6
IL_4NXN_0311/A/662:666,
1/A/740:743		Tandem non-canonical cWW pairs
homologous
IL_4LFB_029
IL_85033.2
IL_4NXN_0641/A/673:677,
1/A/713:717		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
IL_49751.4
IL_4NXN_0331/A/683:688,
1/A/699:707		Kink-turn
homologous
IL_4LFB_031
IL_95727.1
IL_4NXN_0341/A/774:778,
1/A/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.2
IL_4NXN_0351/A/779:783,
1/A/799:803		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_17136.7
IL_4NXN_0361/A/887:894,
1/A/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_4NXN_0721/A/922:923,
1/A/1393:1395		Single bulged A
homologous
IL_5J7L_039
IL_31462.5
IL_4NXN_0381/A/925:927,
1/A/1390:1391		Single bulged G
homologous
IL_4LFB_036
IL_00225.13
IL_4NXN_0391/A/933:935,
1/A/1380:1384		Minor groove platform
homologous
IL_5J7L_041
IL_47078.3
IL_4NXN_0401/A/953:954,
1/A/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.2
IL_4NXN_0411/A/993:999,
1/A/1042:1045		No text annotation
IL_4NXN_0421/A/1007:1009,
1/A/1020:1021		Single stack bend
geometric
IL_4V83_236
IL_90729.1
IL_4NXN_0431/A/1048:1050,
1/A/1208:1209		Single bulged U
geometric
IL_4LFB_042
IL_89505.4
IL_4NXN_0451/A/1052:1056,
1/A/1204:1206		Isolated cWS basepair
geometric
IL_4LFB_044
IL_76319.5
IL_4NXN_0461/A/1057:1058,
1/A/1199:1203		Minor groove platform
homologous
IL_4LFB_045
IL_95583.2
IL_4NXN_0471/A/1060:1061,
1/A/1195:1197		Single bulged U
homologous
IL_6CZR_156
NA
IL_4NXN_0481/A/1061:1063,
1/A/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_28037.2
IL_4NXN_0491/A/1122:1128,
1/A/1143:1151		No text annotation
IL_4NXN_0731/A/1123:1133,
1/A/1141:1150		No text annotation
IL_4NXN_0501/A/1128:1133,
1/A/1141:1143		No text annotation
geometric
IL_4LFB_066
NA
IL_4NXN_0511/A/1247:1253,
1/A/1284:1290		No text annotation
homologous
IL_4LFB_051
IL_09129.2
IL_4NXN_0521/A/1255:1258,
1/A/1277:1282		180 degree turn
homologous
IL_6CZR_161
NA
IL_4NXN_0531/A/1259:1260,
1/A/1274:1276		Not an internal loop
geometric
IL_4LFB_053
NA
IL_4NXN_0671/A/1259:1262,
1/A/1273:1276		Double sheared
homologous
IL_4LFB_067
IL_09705.15
IL_4NXN_0541/A/1260:1262,
1/A/1273:1274		Minor groove platform
homologous
IL_4LFB_054
IL_51454.2
IL_4NXN_0681/A/1303:1308,
1/A/1329:1334		No text annotation
homologous
IL_4LFB_055
IL_85536.2
IL_4NXN_0561/A/1399:1401,
1/A/1501:1504		No text annotation
homologous
IL_4LFB_056
IL_61438.4
IL_4NXN_0691/A/1401:1404,
1/A/1497:1501		No text annotation
geometric
IL_7VYX_002
IL_85033.2
IL_4NXN_0701/A/1404:1407,
1/A/1494:1497		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001
IL_85033.2
IL_4NXN_0711/A/1407:1409,
1/A/1491:1494		No text annotation
geometric
IL_8UO6_002
IL_31737.3
IL_4NXN_0581/A/1412:1414,
1/A/1486:1488		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_87907.2
IL_4NXN_0591/A/1416:1419,
1/A/1481:1484		Double sheared
homologous
IL_4LFB_060
IL_09705.15
IL_4NXN_0601/A/1431:1435,
1/A/1466:1469		UAA/GAN variation
geometric
IL_4LFB_062
IL_77691.5
IL_4NXN_0611/A/1435:1437,
1/A/1464:1466		Isolated non-canonical cWW pair
homologous
IL_4LFB_063
IL_87907.2
IL_4NXN_0621/A/1440:1447,
1/A/1459:1461		No text annotation
homologous
IL_4LFB_064
IL_49061.1

Problematic loops

#loop idProblemSequence
IL_4NXN_007No text annotation
IL_4NXN_008No text annotation
IL_4NXN_019No text annotation
IL_4NXN_032No text annotation
IL_4NXN_037Isolated non-canonical cWW pair
IL_4NXN_065Tandem non-canonical cWW pairs
IL_4NXN_044No text annotation
IL_4NXN_066No text annotation
IL_4NXN_055No text annotation
IL_4NXN_057No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4NXN_0101/A/46:47,
1/A/361:367,
1/A/393:395		No text annotation
geometric
J3_4LFB_010
J3_67856.4
J3_4NXN_0141/A/46:52,
1/A/359:367,
1/A/393:395		No text annotation
homologous
J3_4LFB_014
J3_46317.4
J3_4NXN_0111/A/586:588,
1/A/651:654,
1/A/754:755		No text annotation
geometric
J3_6CZR_016
NA
J3_4NXN_0151/A/586:588,
1/A/651:655,
1/A/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.4
J3_4NXN_0121/A/672:673,
1/A/717:725,
1/A/732:734		No text annotation
homologous
J3_4LFB_012
J3_11934.4
J3_4NXN_0011/A/826:829,
1/A/857:861,
1/A/868:874		No text annotation
homologous
J3_4LFB_001
J3_85054.4
J3_4NXN_0021/A/936:939,
1/A/1344:1350,
1/A/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_4NXN_0031/A/943:946,
1/A/1235:1237,
1/A/1337:1340		No text annotation
homologous
J3_5J7L_005
J3_52655.4
J3_4NXN_0161/A/955:962,
1/A/973:984,
1/A/1221:1225		No text annotation
homologous
J3_4LFB_004
J3_83516.4
J3_4NXN_0051/A/990:993,
1/A/1045:1047,
1/A/1210:1215		No text annotation
homologous
J3_4LFB_005
J3_82572.1
J3_4NXN_0201/A/990:997,
1/A/1044:1047,
1/A/1210:1215		No text annotation
homologous
J3_4LFB_016
J3_76475.2
J3_4NXN_0061/A/1001:1007,
1/A/1021:1029,
1/A/1032:1040		No text annotation
J3_4NXN_0211/A/1002:1009,
1/A/1020:1029,
1/A/1032:1039		No text annotation
J3_4NXN_0071/A/1063:1068,
1/A/1107:1113,
1/A/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_08394.3
J3_4NXN_0191/A/1073:1074,
1/A/1083:1086,
1/A/1099:1102		No text annotation
homologous
J3_4LFB_017
J3_79369.1
J3_4NXN_0081/A/1116:1118,
1/A/1155:1161,
1/A/1175:1184		No text annotation
homologous
J3_4LFB_018
J3_17791.2
J3_4NXN_0091/A/1237:1241,
1/A/1296:1303,
1/A/1334:1337		No text annotation
homologous
J3_4LFB_009
J3_37047.6
J4_4NXN_0011/A/115:122,
1/A/239:240,
1/A/286:289,
1/A/311:312		No text annotation
homologous
J4_4LFB_001
J4_35578.3
J4_4NXN_0021/A/142:144,
1/A/178:183,
1/A/194:198,
1/A/219:221		No text annotation
homologous
J4_4LFB_002
J4_88771.1
J4_4NXN_0031/A/575:577,
1/A/764:769,
1/A/810:821,
1/A/879:880		No text annotation
homologous
J4_4LFB_003
J4_61885.6
J5_4NXN_0011/A/36:39,
1/A/403:406,
1/A/436:442,
1/A/492:500,
1/A/545:548		No text annotation
homologous
J5_4LFB_001
J5_70703.1
J5_4NXN_0021/A/58:61,
1/A/106:113,
1/A/314:316,
1/A/337:339,
1/A/350:354		No text annotation
homologous
J5_4LFB_002
J5_59910.6

Problematic loops

#loop idProblemSequence
J3_4NXN_004No text annotation
J3_4NXN_017No text annotation
J3_4NXN_018No text annotation

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