RNA 3D Hub //

5AJ4 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5AJ4_0011/AA/8:18No text annotation
homologous
HL_4LFB_001
HL_73535.2
HL_5AJ4_0051/AA/147:153No text annotation
geometric
HL_5J7L_018
NA
HL_5AJ4_0081/AA/248:253GNRA
geometric
HL_1G1X_003
NA
HL_5AJ4_0091/AA/342:351No text annotation
homologous
HL_4LFB_015
HL_38491.3
HL_5AJ4_0101/AA/376:381GNRA
homologous
HL_4LFB_016
HL_34789.5
HL_5AJ4_0111/AA/426:436No text annotation
homologous
HL_4LFB_017
HL_38491.3
HL_5AJ4_0691/AA/467:477No text annotation
HL_5AJ4_0131/AA/501:506Mini UNCG
geometric
HL_4ZLD_001
HL_12626.2
HL_5AJ4_0141/AA/568:577No text annotation
homologous
HL_5J7L_021
NA
HL_5AJ4_0161/AA/636:641Mini UNCG
geometric
HL_5AH5_007
HL_90436.4
HL_5AJ4_0171/AA/664:670Pseudoknot geometry
geometric
HL_4GXY_003
HL_97725.1
HL_5AJ4_0201/AA/800:810No text annotation
homologous
HL_4LFB_030
HL_86432.2
HL_5AJ4_0221/AA/941:946GNRA
homologous
HL_4LFB_032
HL_34789.5
HL_5AJ4_0701/BA/54:61No text annotation
geometric
HL_8CRE_001
NA
HL_5AJ4_0231/BA/80:86No text annotation
geometric
HL_5J7L_141
NA
HL_5AJ4_0241/BA/121:126GNRA
homologous
HL_7RQB_015
NA
HL_5AJ4_0251/BA/166:174No text annotation
homologous
HL_7RQB_017
NA
HL_5AJ4_0261/BA/182:191T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_5AJ4_0271/BA/219:224No text annotation
geometric
HL_7A0S_011
HL_75660.9
HL_5AJ4_0641/BA/269:276No text annotation
geometric
HL_8C3A_039
NA
HL_5AJ4_0291/BA/290:299No text annotation
homologous
HL_7RQB_023
NA
HL_5AJ4_0301/BA/325:331No text annotation
homologous
HL_7RQB_024
NA
HL_5AJ4_0311/BA/371:376No text annotation
homologous
HL_4WF9_025
HL_27530.2
HL_5AJ4_0321/BA/400:409Externally structured
geometric
HL_8C3A_022
NA
HL_5AJ4_0331/BA/441:448GNRA
homologous
HL_4WF9_027
HL_34789.5
HL_5AJ4_0341/BA/461:468No text annotation
homologous
HL_5J7L_160
NA
HL_5AJ4_0371/BA/611:618tRNA D-loop
geometric
HL_1FIR_001
NA
HL_5AJ4_0651/BA/652:655Mini UNCG
geometric
HL_8SP9_002
HL_12626.2
HL_5AJ4_0391/BA/686:691No text annotation
geometric
HL_5TBW_044
NA
HL_5AJ4_0401/BA/729:732No text annotation
geometric
HL_7RQB_039
NA
HL_5AJ4_0411/BA/758:765No text annotation
homologous
HL_7RQB_040
NA
HL_5AJ4_0421/BA/827:837No text annotation
homologous
HL_4WF9_043
HL_87681.2
HL_5AJ4_0431/BA/848:862No text annotation
HL_5AJ4_0461/BA/942:950No text annotation
homologous
HL_7A0S_048
HL_33350.1
HL_5AJ4_0471/BA/1020:1029No text annotation
homologous
HL_4WF9_047
HL_78372.2
HL_5AJ4_0491/BA/1146:1154LSU P loop
homologous
HL_7A0S_052
HL_11974.3
HL_5AJ4_0501/BA/1162:1174No text annotation
HL_5AJ4_0511/BA/1185:1188Mini UNCG
geometric
HL_4V88_192
NA
HL_5AJ4_0521/BA/1196:1203GNRA with extra cWW
geometric
HL_4WF9_053
HL_87268.3
HL_5AJ4_0531/BA/1236:1241No text annotation
geometric
HL_4V9F_003
HL_75660.9
HL_5AJ4_0541/BA/1292:1300No text annotation
homologous
HL_5J7L_193
NA
HL_5AJ4_0551/BA/1349:1356No text annotation
homologous
HL_7RQB_061
NA
HL_5AJ4_0561/BA/1372:1378LSU A loop
homologous
HL_4WF9_058
HL_48677.2
HL_5AJ4_0571/BA/1415:1420GNRA
homologous
HL_7RQB_063
NA
HL_5AJ4_0661/BA/1452:1470No text annotation
HL_5AJ4_0591/BA/1487:1493No text annotation
HL_5AJ4_0601/BA/1512:1530No text annotation
HL_5AJ4_0611/BA/1555:1563No text annotation
geometric
HL_7A0S_067
HL_37889.2
HL_5AJ4_0681/BB/32:40tRNA anticodon loop
geometric
HL_2AZX_005
NA

Problematic loops

#loop idProblemSequence
HL_5AJ4_002No text annotation
HL_5AJ4_003No text annotation
HL_5AJ4_062No text annotation
HL_5AJ4_004No text annotation
HL_5AJ4_006No text annotation
HL_5AJ4_007GNRA
HL_5AJ4_012No text annotation
HL_5AJ4_063No text annotation
HL_5AJ4_015No text annotation
HL_5AJ4_018No text annotation
HL_5AJ4_019T-loop with 2 stacked bulged bases
HL_5AJ4_021No text annotation
HL_5AJ4_028GNRA with tandem sheared
HL_5AJ4_035No text annotation
HL_5AJ4_036GNRA with tandem sheared
HL_5AJ4_038No text annotation
HL_5AJ4_044No text annotation
HL_5AJ4_045No text annotation
HL_5AJ4_048No text annotation
HL_5AJ4_058GNRA
HL_5AJ4_067No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5AJ4_0011/AA/3:5,
1/AA/21:22		No text annotation
IL_5AJ4_0021/AA/39:40,
1/AA/215:217		Single bulged A
homologous
IL_5J7L_002
NA
IL_5AJ4_0041/AA/48:50,
1/AA/175:176		Minor groove platform
homologous
IL_5J7L_004
NA
IL_5AJ4_0051/AA/78:79,
1/AA/103:105		Minor groove platform
geometric
IL_6DTD_003
IL_34520.4
IL_5AJ4_1121/AA/110:115,
1/AA/135:142		Kink-turn with non-sequential stacking
geometric
IL_4LFB_011
IL_46174.5
IL_5AJ4_0081/AA/116:119,
1/AA/133:134		Major groove platform; stack outside cWW
geometric
IL_1NTA_003
IL_74641.3
IL_5AJ4_1051/AA/116:120,
1/AA/131:134		No text annotation
IL_5AJ4_0091/AA/119:120,
1/AA/131:133		No text annotation
IL_5AJ4_0131/AA/226:228,
1/AA/269:271		No text annotation
geometric
IL_3LA5_001
NA
IL_5AJ4_0141/AA/230:239,
1/AA/264:267		No text annotation
IL_5AJ4_0151/AA/241:247,
1/AA/254:262		Kink-turn related
geometric
IL_4V88_415
NA
IL_5AJ4_0161/AA/290:296,
1/AA/484:485		No text annotation
homologous
IL_5J7L_026
NA
IL_5AJ4_0171/AA/301:305,
1/AA/397:401		UAA/GAN
geometric
IL_4V9F_037
IL_08938.2
IL_5AJ4_1061/AA/306:321,
1/AA/389:396		No text annotation
IL_5AJ4_0181/AA/327:334,
1/AA/360:367		No text annotation
IL_5AJ4_0191/AA/339:341,
1/AA/352:355		No text annotation
IL_5AJ4_0201/AA/373:375,
1/AA/382:383		Other IL
geometric
IL_3WBM_004
IL_18188.1
IL_5AJ4_0211/AA/414:418,
1/AA/444:445		Left turn
homologous
IL_5J7L_036
NA
IL_5AJ4_0221/AA/419:423,
1/AA/439:443		tSH-tWH-tHS
homologous
IL_5J7L_037
NA
IL_5AJ4_0231/AA/491:500,
1/AA/507:514		10x8 Sarcin-Ricin; G-bulge
geometric
IL_6UFM_002
IL_22278.1
IL_5AJ4_0241/AA/526:527,
1/AA/837:839		Single bulged A
homologous
IL_5J7L_039
NA
IL_5AJ4_0251/AA/529:531,
1/AA/834:835		Single bulged G
homologous
IL_4LFB_036
IL_28408.3
IL_5AJ4_0261/AA/537:541,
1/AA/824:828		No text annotation
IL_5AJ4_0271/AA/559:560,
1/AA/710:712		Minor groove platform
homologous
IL_4LFB_038
IL_34520.4
IL_5AJ4_1081/AA/595:607,
1/AA/695:700		No text annotation
IL_5AJ4_0281/AA/608:610,
1/AA/693:694		Single bulged U
homologous
IL_5J7L_046
NA
IL_5AJ4_0291/AA/612:616,
1/AA/689:691		Isolated cWS basepair
homologous
IL_4LFB_044
IL_82453.2
IL_5AJ4_0301/AA/617:618,
1/AA/684:688		Minor groove platform
homologous
IL_6CZR_155
NA
IL_5AJ4_0311/AA/620:621,
1/AA/680:682		Single bulged A
geometric
IL_5J7L_049
NA
IL_5AJ4_0321/AA/621:623,
1/AA/678:680		Isolated non-canonical cWW pair
homologous
IL_5J7L_050
NA
IL_5AJ4_0331/AA/629:632,
1/AA/652:655		Tandem non-canonical cWW pairs
geometric
IL_5C5W_001
IL_71194.3
IL_5AJ4_0341/AA/633:634,
1/AA/643:651		Multiple bulged bases
geometric
IL_1R3E_002
IL_05670.1
IL_5AJ4_0351/AA/749:754,
1/AA/773:778		No text annotation
IL_5AJ4_0361/AA/843:845,
1/AA/927:930		No text annotation
homologous
IL_5J7L_058
NA
IL_5AJ4_0371/AA/845:848,
1/AA/923:927		No text annotation
geometric
IL_4V88_464
NA
IL_5AJ4_0381/AA/849:851,
1/AA/920:922		Isolated non-canonical cWW pair
geometric
IL_5MWI_007
NA
IL_5AJ4_0391/AA/851:855,
1/AA/915:920		No text annotation
IL_5AJ4_1131/AA/857:859,
1/AA/911:913		Isolated non-canonical cWW pair
homologous
IL_6CZR_411
NA
IL_5AJ4_0411/AA/860:863,
1/AA/907:910		Double sheared
homologous
IL_5J7L_062
NA
IL_5AJ4_0441/BA/2:4,
1/BA/146:151		No text annotation
IL_5AJ4_0461/BA/12:13,
1/BA/103:105		Single bulged C
geometric
IL_7KGA_004
IL_05642.4
IL_5AJ4_0481/BA/70:73,
1/BA/92:95		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
IL_71194.3
IL_5AJ4_0491/BA/73:79,
1/BA/87:92		7x6 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_251
NA
IL_5AJ4_0501/BA/180:182,
1/BA/191:193		Isolated non-canonical cWW pair
homologous
IL_5J7L_257
NA
IL_5AJ4_0511/BA/213:215,
1/BA/229:231		Isolated non-canonical cWW pair
geometric
IL_4LFB_063
IL_01003.5
IL_5AJ4_0521/BA/215:218,
1/BA/225:229		No text annotation
IL_5AJ4_0531/BA/239:241,
1/BA/352:354		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.5
IL_5AJ4_0541/BA/241:245,
1/BA/345:352		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_5AJ4_0551/BA/248:250,
1/BA/340:342		No text annotation
geometric
IL_3LA5_001
NA
IL_5AJ4_0561/BA/258:260,
1/BA/315:317		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_01003.5
IL_5AJ4_0571/BA/264:265,
1/BA/309:311		Single bulged A
homologous
IL_5J7L_261
NA
IL_5AJ4_0581/BA/284:287,
1/BA/302:304		Major groove platform with extra cWW
homologous
IL_7A0S_019
IL_36931.3
IL_5AJ4_0591/BA/321:323,
1/BA/333:337		Multiple bulged bases
homologous
IL_7RQB_023
NA
IL_5AJ4_0601/BA/393:399,
1/BA/410:416		No text annotation
IL_5AJ4_0611/BA/477:479,
1/BA/586:587		Single bulged C
homologous
IL_5J7L_276
NA
IL_5AJ4_0641/BA/529:532,
1/BA/543:544		No text annotation
homologous
IL_6PRV_002
NA
IL_5AJ4_0651/BA/638:645,
1/BA/1004:1010		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_5AJ4_0661/BA/661:664,
1/BA/771:777		No text annotation
IL_5AJ4_0671/BA/680:685,
1/BA/692:695		C-loop
homologous
IL_7RQB_051
NA
IL_5AJ4_0681/BA/708:711,
1/BA/741:749		No text annotation
IL_5AJ4_0691/BA/717:729,
1/BA/732:735		No text annotation
IL_5AJ4_0701/BA/785:790,
1/BA/996:998		No text annotation
IL_5AJ4_0711/BA/796:798,
1/BA/988:990		Isolated tWW turn
homologous
IL_7A0S_060
IL_10432.2
IL_5AJ4_0721/BA/799:802,
1/BA/986:987		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_5AJ4_1111/BA/799:807,
1/BA/983:987		No text annotation
homologous
IL_4WF9_117
IL_80252.2
IL_5AJ4_0731/BA/802:807,
1/BA/983:986		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.2
IL_5AJ4_0741/BA/807:815,
1/BA/980:983		No text annotation
IL_5AJ4_0751/BA/820:821,
1/BA/973:975		Single bulged A
homologous
IL_7RQB_069
NA
IL_5AJ4_0761/BA/871:872,
1/BA/967:969		Single stack bend
geometric
IL_7KGA_003
IL_15011.4
IL_5AJ4_0771/BA/878:881,
1/BA/896:897		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_5AJ4_0781/BA/882:883,
1/BA/892:895		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_5AJ4_0791/BA/926:927,
1/BA/957:960		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_5AJ4_0801/BA/927:938,
1/BA/954:957		No text annotation
IL_5AJ4_0811/BA/1043:1045,
1/BA/1438:1439		Major groove platform
homologous
IL_5J7L_320
NA
IL_5AJ4_0821/BA/1047:1049,
1/BA/1433:1436		No text annotation
homologous
IL_4WF9_079
IL_80025.2
IL_5AJ4_0831/BA/1060:1062,
1/BA/1263:1264		Single bulged U
homologous
IL_7RQB_080
NA
IL_5AJ4_0841/BA/1063:1064,
1/BA/1259:1262		Minor groove platform
homologous
IL_4WF9_081
IL_34520.4
IL_5AJ4_0851/BA/1073:1076,
1/BA/1136:1138		No text annotation
geometric
IL_4V9F_053
IL_49140.1
IL_5AJ4_0861/BA/1078:1080,
1/BA/1132:1134		Isolated non-canonical cWW pair
homologous
IL_5J7L_326
NA
IL_5AJ4_0871/BA/1083:1085,
1/BA/1124:1129		No text annotation
IL_5AJ4_0881/BA/1190:1192,
1/BA/1206:1209		Minor groove platform with extra cWW
geometric
IL_7RQB_031
NA
IL_5AJ4_0891/BA/1192:1194,
1/BA/1205:1206		Minor groove platform
geometric
IL_4V88_412
NA
IL_5AJ4_0901/BA/1274:1275,
1/BA/1319:1321		Single stack bend
homologous
IL_4WF9_089
IL_15011.4
IL_5AJ4_0911/BA/1275:1276,
1/BA/1317:1319		Major groove platform
geometric
IL_7RQB_092
NA
IL_5AJ4_0921/BA/1277:1280,
1/BA/1314:1316		Major groove platform with extra pair
homologous
IL_7RQB_093
NA
IL_5AJ4_0931/BA/1280:1282,
1/BA/1310:1314		Major groove minor groove platform with extra cWW
geometric
IL_5J7L_337
NA
IL_5AJ4_0941/BA/1287:1291,
1/BA/1301:1305		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
NA
IL_5AJ4_0951/BA/1328:1329,
1/BA/1401:1403		Major groove platform
homologous
IL_7RQB_096
NA
IL_5AJ4_0961/BA/1331:1333,
1/BA/1395:1399		Isolated non-canonical cWW with bulges
homologous
IL_4WF9_095
IL_68118.5
IL_5AJ4_0971/BA/1333:1334,
1/BA/1392:1395		No text annotation
geometric
IL_5J7L_341
NA
IL_5AJ4_0981/BA/1342:1344,
1/BA/1361:1365		No text annotation
IL_5AJ4_0991/BA/1412:1413,
1/BA/1422:1424		Single bulged A
homologous
IL_7RQB_101
NA
IL_5AJ4_1011/BA/1452:1459,
1/BA/1464:1470		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_5AJ4_1021/BA/1481:1485,
1/BA/1495:1497		C-loop
geometric
IL_7RQB_051
NA
IL_5AJ4_1031/BA/1485:1487,
1/BA/1493:1495		Isolated non-canonical cWW pair
geometric
IL_6IA2_005
IL_01003.5
IL_5AJ4_1041/BA/1505:1510,
1/BA/1532:1537		No text annotation
geometric
IL_4QLM_002
IL_74322.2

Problematic loops

#loop idProblemSequence
IL_5AJ4_003Single bulged A
IL_5AJ4_006Double sheared with non-canonical cWW
IL_5AJ4_007No text annotation
IL_5AJ4_010Isolated non-canonical cWW pair
IL_5AJ4_011C-loop
IL_5AJ4_012Single bulged G
IL_5AJ4_107Isolated non-canonical cWW pair
IL_5AJ4_040Tandem non-canonical cWW pairs
IL_5AJ4_042No text annotation
IL_5AJ4_109No text annotation
IL_5AJ4_043No text annotation
IL_5AJ4_110No text annotation
IL_5AJ4_114No text annotation
IL_5AJ4_045No text annotation
IL_5AJ4_047No text annotation
IL_5AJ4_062Isolated non-canonical cWW pair
IL_5AJ4_063No text annotation
IL_5AJ4_100Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5AJ4_0011/AA/31:34,
1/AA/222:226,
1/AA/271:274		No text annotation
J3_5AJ4_0021/AA/41:44,
1/AA/179:186,
1/AA/212:214		No text annotation
J3_5AJ4_0131/AA/326:327,
1/AA/367:373,
1/AA/383:384		No text annotation
J3_5AJ4_0141/AA/542:545,
1/AA/788:794,
1/AA/816:823		No text annotation
homologous
J3_5J7L_052
NA
J3_5AJ4_0031/AA/549:552,
1/AA/719:721,
1/AA/781:784		No text annotation
homologous
J3_4LFB_003
J3_44359.2
J3_5AJ4_0041/AA/561:567,
1/AA/578:589,
1/AA/706:709		No text annotation
J3_5AJ4_0051/AA/595:598,
1/AA/605:607,
1/AA/695:700		No text annotation
homologous
J3_5J7L_007
NA
J3_5AJ4_0061/AA/623:628,
1/AA/656:663,
1/AA/671:678		No text annotation
J3_5AJ4_0151/BA/8:11,
1/BA/106:120,
1/BA/127:131		No text annotation
J3_5AJ4_0081/BA/250:256,
1/BA/319:321,
1/BA/337:340		No text annotation
homologous
J3_4WF9_002
J3_46658.2
J3_5AJ4_0091/BA/265:267,
1/BA/278:282,
1/BA/306:309		No text annotation
homologous
J3_7RQB_005
NA
J3_5AJ4_0161/BA/481:502,
1/BA/522:529,
1/BA/544:584		No text annotation
J3_5AJ4_0101/BA/667:674,
1/BA/753:757,
1/BA/766:768		No text annotation
J3_5AJ4_0111/BA/674:676,
1/BA/699:706,
1/BA/751:753		No text annotation
J3_5AJ4_0171/BA/1180:1181,
1/BA/1223:1234,
1/BA/1243:1249		No text annotation
J3_5AJ4_0121/BA/1338:1341,
1/BA/1366:1368,
1/BA/1382:1388		No text annotation
homologous
J3_9DFE_017
J3_32601.6
J4_5AJ4_0011/AA/52:55,
1/AA/62:69,
1/AA/156:158,
1/AA/167:173		No text annotation
J4_5AJ4_0021/AA/71:77,
1/AA/106:108,
1/AA/144:147,
1/AA/153:154		No text annotation
J4_5AJ4_0031/AA/296:298,
1/AA/404:409,
1/AA/450:461,
1/AA/483:484		No text annotation
homologous
J4_5J7L_003
NA
J4_5AJ4_0041/BA/646:649,
1/BA/658:659,
1/BA/779:782,
1/BA/1001:1003		No text annotation
J4_5AJ4_0051/BA/667:676,
1/BA/699:706,
1/BA/751:757,
1/BA/766:768		No text annotation
J4_5AJ4_0061/BA/822:826,
1/BA/838:843,
1/BA/867:872,
1/BA/967:972		No text annotation
J4_5AJ4_0071/BA/874:876,
1/BA/899:900,
1/BA/917:926,
1/BA/960:965		No text annotation
homologous
J4_5J7L_026
NA
J4_5AJ4_0081/BA/1444:1446,
1/BA/1476:1477,
1/BA/1501:1503,
1/BA/1539:1541		No text annotation
J4_5AJ4_0101/BB/7:10,
1/BB/26:28,
1/BB/44:49,
1/BB/62:63		No text annotation
J5_5AJ4_0041/BA/200:209,
1/BA/235:238,
1/BA/355:358,
1/BA/603:607,
1/BA/622:632		No text annotation
J5_5AJ4_0051/BA/1050:1057,
1/BA/1267:1274,
1/BA/1321:1328,
1/BA/1403:1409,
1/BA/1427:1432		No text annotation
J5_5AJ4_0031/BA/1067:1070,
1/BA/1141:1144,
1/BA/1156:1157,
1/BA/1179:1180,
1/BA/1249:1256		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_5AJ4_0011/BA/362:368,
1/BA/379:383,
1/BA/426:433,
1/BA/456:460,
1/BA/469:474,
1/BA/590:599		No text annotation
J6_5AJ4_0021/BA/1067:1070,
1/BA/1141:1144,
1/BA/1156:1157,
1/BA/1179:1181,
1/BA/1223:1234,
1/BA/1243:1256		No text annotation

Problematic loops

#loop idProblemSequence
J3_5AJ4_018No text annotation
J3_5AJ4_007No text annotation
J4_5AJ4_009No text annotation
J5_5AJ4_001No text annotation
J5_5AJ4_002No text annotation

Coloring options:
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